Added annotations to identifiers, and converted the unused annotationtest.py to

test the new module.

test/system/annotationtest.py

@@ -1,32 +1,57 @@
 
 import unittest
 import sys
-sys.path.append('../../system')
-from annotations import *
-from sets import Set as set
+sys.path.append('../../')
+from fluents import annotations
 
-class AnnotationTest(unittest.TestCase):
+class AnnotationsTest(unittest.TestCase):
 
     def setUp(self):
         pass
 
-    def testCreation(self):
-        a = Annotations('x', 'y')
-
-        assert a.has_dimension('x')        
-        assert a.has_dimension('y')        
-        assert not a.has_dimension('z')        
-
     def testAddAnnotations(self):
-        ann = Annotations('genes', 'go')
-        go = set(['GO:0', 'GO:1'])
-        ann.add_annotations('genes', 'BadGene', 'go', go)
-        genes = set(['BadGene'])
+        h = annotations.DictAnnotationHandler()
+        annotations.set_dim_handler('go-terms', h)
+        assert annotations.get_dim_handler('go-terms') == h
+        assert annotations.get_dim_handler('foobar') == None
 
-        assert ann.get_annotations('genes', 'BadGene', 'go') == go
-        assert ann.get_annotations('go', 'GO:0', 'genes') == genes
-        assert ann.get_annotations('go', 'GO:1', 'genes') == genes
-        assert ann.get_annotations('go', 'GO:2', 'genes') == set()
+    def testGetDimAnnotations(self):
+        h = annotations.DictAnnotationHandler()
+        annotations.set_dim_handler('go-terms', h)
+        d = {'GO:0': 'biological_process',
+             'GO:1': 'foo',
+             'GO:2': 'bar'}
+        h.add_annotations('name', d)
+        
+        ann0 = annotations.get_dim_annotations('go-terms', 'name', [])
+        assert ann0 == []
+
+        ann1 = annotations.get_dim_annotations('go-terms', 'name', ['GO:0'])
+        assert len(ann1) == 1
+        assert ann1[0] == 'biological_process'
+
+        ann2 = annotations.get_dim_annotations('go-terms', 'name', ['GO:1', 'baz'])
+        assert len(ann2) == 2
+        assert ann2 == ['foo', None]
+
+    def testDictAnnotationHandler(self):
+        h = annotations.DictAnnotationHandler()
+        annotations.set_dim_handler('go-terms', h)
+        d = {'GO:0': 'biological_process',
+             'GO:1': 'foo',
+             'GO:2': 'bar'}
+        h.add_annotations('name', d)
+        
+        ann0 = h.get_annotations('name', [])
+        assert ann0 == []
+        
+        ann1 = h.get_annotations('name', ['unexisting'])
+        assert ann1 == [None]
+        
+        ann2 = h.get_annotations('name', ['unexisting'], 42)
+        assert ann2 == [42]
+
+        assert h.get_annotation_names() == ['name']
 
 if __name__ == '__main__':
     unittest.main()