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Vis registry: add two tests (has_attribute, not_eq); add see also for test types in visualization.dtd; correct applicability tests for trackster and circster using not_eq on datatype.track_type

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This commit is contained in:
Carl Eberhard
2014-08-28 09:44:56 -04:00
parent 7543a567f2
commit 7017833f42
4 changed files with 19 additions and 9 deletions
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config/plugins/visualizations/circster/config/circster.xml
+2 -2
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@@ -4,13 +4,13 @@
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<test type="not_eq" test_attr="datatype.track_type">None</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="hda">hda_ldda</to_param>
</data_source>
<data_source>
<model_class>LibraryDatasetDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<test type="not_eq" test_attr="datatype.track_type">None</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="ldda">hda_ldda</to_param>
</data_source>
config/plugins/visualizations/trackster/config/trackster.xml
+2 -2
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@@ -5,14 +5,14 @@
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<test type="not_eq" test_attr="datatype.track_type">None</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="hda">hda_ldda</to_param>
<to_param param_attr="dbkey">dbkey</to_param>
</data_source>
<data_source>
<model_class>LibraryDatasetDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<test type="not_eq" test_attr="datatype.track_type">None</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="ldda">hda_ldda</to_param>
</data_source>
config/plugins/visualizations/visualization.dtd
+2 -1
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@@ -33,7 +33,8 @@
Currently, all tests are OR'd and there is no logical grouping. Tests are run in order.
(text): the text of this element is what the given target will be compared to (REQUIRED)
type: what type of test to run (e.g. when the target is an HDA the test will often be of type 'isinstance'
and test whether the HDA's datatype isinstace of a class)
and test whether the HDA's datatype isinstace of a class).
See lib/galaxy/visualizations/registry.py, DataSourceParser.parse_tests for test type options.
DEFAULT: string comparison.
test_attr: what attribute of the target object should be used in the test. For instance, 'datatype'
will attempt to get the HDA.datatype from a target HDA. If the given object doesn't have
lib/galaxy/visualization/registry.py
+13 -4
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@@ -203,6 +203,7 @@ class VisualizationsRegistry( pluginframework.PageServingPluginManager ):
#log.debug( '\t passed model_class' )
# tests are optional - default is the above class test
#TODO: not true: must have test currently
tests = data_source[ 'tests' ]
if tests and not self.is_object_applicable( trans, target_object, tests ):
continue
@@ -228,14 +229,14 @@ class VisualizationsRegistry( pluginframework.PageServingPluginManager ):
Run a visualization's data_source tests to find out if
it can be applied to the target_object.
"""
#log.debug( 'is_object_applicable( self, trans, %s, %s )', target_object, data_source_tests )
log.debug( 'is_object_applicable( self, trans, %s, %s )', target_object, data_source_tests )
for test in data_source_tests:
test_type = test[ 'type' ]
result_type = test[ 'result_type' ]
test_result = test[ 'result' ]
test_fn = test[ 'fn' ]
#log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
# test_type, result_type, test_result, test_fn )
log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
test_type, result_type, test_result, test_fn )
if test_type == 'isinstance':
# parse test_result based on result_type (curr: only datatype has to do this)
@@ -253,7 +254,7 @@ class VisualizationsRegistry( pluginframework.PageServingPluginManager ):
#NOTE: tests are OR'd, if any test passes - the visualization can be applied
if test_fn( target_object, test_result ):
#log.debug( '\t test passed' )
log.debug( '\t test passed' )
return True
return False
@@ -407,6 +408,7 @@ class VisualizationsConfigParser( object ):
# allow manually turning off a vis by checking for a disabled property
if 'disabled' in xml_tree.attrib:
#TODO: differentiate between disabled and failed to parse, log.warn only on failure, log.info otherwise
return None
# a text display name for end user links
@@ -627,6 +629,13 @@ class DataSourceParser( object ):
test_fn = lambda o, result: ( hasattr( getter( o ), 'has_dataprovider' )
and getter( o ).has_dataprovider( result ) )
elif test_type == 'has_attribute':
# does the object itself have attr in 'result' (no equivalence checking)
test_fn = lambda o, result: hasattr( getter( o ), result )
elif test_type == 'not_eq':
test_fn = lambda o, result: str( getter( o ) ) != result
else:
# default to simple (string) equilavance (coercing the test_attr to a string)
test_fn = lambda o, result: str( getter( o ) ) == result