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Fixes for boolean & select handling in test data elements.
- Allow boolean "truevalue"/"falsevalue" to be used in plain (non-conditional test element) parameters (see https://trello.com/c/iGk3f1pE).
- Fix conditionals to use processed values - so this fix and 5b6c092aa0 are applid to these elements as well. (http://osdir.com/ml/general/2015-05/msg24402.html).
This also adds tests to verify these behaviors.
Run most relevant tests with commands:
./run_tests.sh -framework -id simple_constructs
./run_tests.sh -framework -id multi_select
./run_tests.sh -framework -id boolean_conditional
This commit is contained in:
John Chilton
+53
-30
@@ -71,9 +71,8 @@ class ToolTestBuilder( object ):
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# No explicit value for param in test case, determine from default
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query_value = test_param.checked
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else:
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# Test case supplied value, check cases against this.
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query_value = string_as_bool( declared_value )
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matches_declared_value = lambda case_value: string_as_bool(case_value) == query_value
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query_value = _process_bool_param_value( test_param, declared_value )
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matches_declared_value = lambda case_value: _process_bool_param_value( test_param, case_value ) == query_value
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elif isinstance(test_param, galaxy.tools.parameters.basic.SelectToolParameter):
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if declared_value is not None:
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# Test case supplied explicit value to check against.
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@@ -166,7 +165,8 @@ class ToolTestBuilder( object ):
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# as a new instance with value defined and hence enter
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# an infinite loop - hence the "case_value is not None"
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# check.
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expanded_inputs[ case_context.for_state() ] = expanded_case_value
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processed_value = _process_simple_value( value.test_param, expanded_case_value )
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expanded_inputs[ case_context.for_state() ] = processed_value
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elif isinstance( value, galaxy.tools.parameters.grouping.Section ):
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context = ParamContext( name=value.name, parent_context=parent_context )
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for r_name, r_value in value.inputs.iteritems():
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@@ -203,33 +203,8 @@ class ToolTestBuilder( object ):
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for ( name, value, extra ) in collection_def.collect_inputs():
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require_file( name, value, extra, self.required_files )
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processed_value = collection_def
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elif isinstance( value, galaxy.tools.parameters.basic.SelectToolParameter ) and hasattr( value, 'static_options' ):
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# Tests may specify values as either raw value or the value
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# as they appear in the list - the API doesn't and shouldn't
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# accept the text value - so we need to convert the text
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# into the form value.
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def process_param_value( param_value ):
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found_value = False
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value_for_text = None
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if value.static_options:
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for (text, opt_value, selected) in value.static_options:
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if param_value == opt_value:
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found_value = True
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if value_for_text is None and param_value == text:
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value_for_text = opt_value
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if not found_value and value_for_text is not None:
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processed_value = value_for_text
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else:
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processed_value = param_value
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return processed_value
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# Do replacement described above for lists or singleton
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# values.
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if isinstance( param_value, list ):
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processed_value = map( process_param_value, param_value )
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else:
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processed_value = process_param_value( param_value )
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else:
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processed_value = param_value
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processed_value = _process_simple_value( value, param_value )
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expanded_inputs[ context.for_state() ] = processed_value
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return expanded_inputs
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@@ -240,6 +215,54 @@ class ToolTestBuilder( object ):
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return require_file( name, value, extra, self.required_files )
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def _process_simple_value( param, param_value ):
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if isinstance( param, galaxy.tools.parameters.basic.SelectToolParameter ) and hasattr( param, 'static_options' ):
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# Tests may specify values as either raw value or the value
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# as they appear in the list - the API doesn't and shouldn't
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# accept the text value - so we need to convert the text
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# into the form value.
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def process_param_value( param_value ):
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found_value = False
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value_for_text = None
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if param.static_options:
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for (text, opt_value, selected) in param.static_options:
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if param_value == opt_value:
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found_value = True
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if value_for_text is None and param_value == text:
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value_for_text = opt_value
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if not found_value and value_for_text is not None:
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processed_value = value_for_text
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else:
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processed_value = param_value
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return processed_value
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# Do replacement described above for lists or singleton
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# values.
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if isinstance( param_value, list ):
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processed_value = map( process_param_value, param_value )
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else:
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processed_value = process_param_value( param_value )
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elif isinstance( param, galaxy.tools.parameters.basic.BooleanToolParameter ):
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# Like above, tests may use the tool define values of simply
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# true/false.
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processed_value = _process_bool_param_value( param, param_value )
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else:
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processed_value = param_value
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return processed_value
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def _process_bool_param_value( param, param_value ):
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assert isinstance( param, galaxy.tools.parameters.basic.BooleanToolParameter )
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if isinstance( param_value, list ):
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param_value = param_value[0]
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if param.truevalue == param_value:
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processed_value = True
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elif param.falsevalue == param_value:
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processed_value = False
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else:
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processed_value = string_as_bool( param_value )
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return processed_value
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@nottest
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def test_data_iter( required_files ):
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for fname, extra in required_files:
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@@ -0,0 +1,53 @@
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<tool id="boolean_conditional" name="boolean_conditional" version="1.0.0">
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<command>
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echo "$p1.p1val" >> $out_file1;
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</command>
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<inputs>
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<conditional name="p1">
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<param type="boolean" name="p1use" truevalue="booltrue" falsevalue="boolfalse" />
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<when value="booltrue">
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<param name="p1val" value="p1used" type="text" />
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</when>
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<when value="boolfalse">
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<param name="p1val" value="p1notused" type="text" />
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data name="out_file1" format="txt" />
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</outputs>
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<tests>
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<test>
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<param name="p1use" value="true" />
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<output name="out_file1">
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<assert_contents>
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<has_line line="p1used" />
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</assert_contents>
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</output>
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</test>
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<test>
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<param name="p1use" value="booltrue" />
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<output name="out_file1">
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<assert_contents>
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<has_line line="p1used" />
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</assert_contents>
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</output>
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</test>
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<test>
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<param name="p1use" value="false" />
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<output name="out_file1">
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<assert_contents>
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<has_line line="p1notused" />
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</assert_contents>
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</output>
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</test>
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<test>
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<param name="p1use" value="boolfalse" />
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<output name="out_file1">
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<assert_contents>
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<has_line line="p1notused" />
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</assert_contents>
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</output>
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</test>
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</tests>
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</tool>
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@@ -3,6 +3,7 @@
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<tool file="upload.xml"/>
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<tool file="simple_constructs.xml" />
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<tool file="inheritance_simple.xml" />
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<tool file="boolean_conditional.xml" />
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<tool file="composite.xml" />
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<tool file="compare_bam_as_sam.xml" />
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<tool file="code_file.xml" />
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@@ -61,5 +61,17 @@
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</assert_contents>
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</output>
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</test>
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<test>
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<!-- Again but using boolean's truevalue -->
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<param name="p1use" value="true" />
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<param name="booltest" value="booltrue" />
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<param name="file" value="simple_line.txt" />
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<output name="out_file1">
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<assert_contents>
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<has_line line="p1used" />
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<has_line line="booltrue" />
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</assert_contents>
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</output>
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</test>
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</tests>
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</tool>
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