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

test the new module.

fluents/annotations.py

@@ -0,0 +1,60 @@
+
+from fluents import dataset
+
+_dim_annotation_handlers = {}
+
+def get_dim_annotations(dimname, annotation, ids):
+    """Returns a list of annotations corresponding to the given ids in 
+    dimension dimname"""
+    global _dim_annotation_handlers
+
+    if _dim_annotation_handlers.has_key(dimname):
+        return _dim_annotation_handlers[dimname].get_annotations(annotation, ids)
+    return None
+
+def set_dim_handler(dimname, handler):
+    """Set the handler for the given dimension."""
+    global _dim_annotation_handlers
+    _dim_annotation_handlers[dimname] = handler
+    
+def get_dim_handler(dimname):
+    """Get the handler for the given dimension."""
+    global _dim_annotation_handlers
+    if _dim_annotation_handlers.has_key(dimname):
+        return _dim_annotation_handlers[dimname]
+    else: 
+        return None
+
+
+class AnnotationHandler:
+    def __init__(self):
+        pass
+
+    def get_annotations(self, annotationname, ids, default=None):
+        return None
+
+    def get_annotation_names(self):
+        return []
+
+
+class DictAnnotationHandler(AnnotationHandler):
+
+    def __init__(self, d={}):
+        self._dict = d
+    
+    def get_annotations(self, annotationname, ids, default=None):
+        d = self._dict
+        retval = []
+        for id in ids:
+            if d[annotationname].has_key(id):
+                retval.append(d[annotationname][id])
+            else:
+                retval.append(default)
+        return retval
+    
+    def add_annotations(self, annotationname, d):
+        self._dict[annotationname] = d
+
+    def get_annotation_names(self):
+        return self._dict.keys()
+        

test/system/annotationtest.py

@@ -1,32 +1,57 @@
 
 import unittest
 import sys
-sys.path.append('../../system')
+sys.path.append('../../')
-from annotations import *
+from fluents import annotations
-from sets import Set as set
 
-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')
+        h = annotations.DictAnnotationHandler()
-        go = set(['GO:0', 'GO:1'])
+        annotations.set_dim_handler('go-terms', h)
-        ann.add_annotations('genes', 'BadGene', 'go', go)
+        assert annotations.get_dim_handler('go-terms') == h
-        genes = set(['BadGene'])
+        assert annotations.get_dim_handler('foobar') == None
 
-        assert ann.get_annotations('genes', 'BadGene', 'go') == go
+    def testGetDimAnnotations(self):
-        assert ann.get_annotations('go', 'GO:0', 'genes') == genes
+        h = annotations.DictAnnotationHandler()
-        assert ann.get_annotations('go', 'GO:1', 'genes') == genes
+        annotations.set_dim_handler('go-terms', h)
-        assert ann.get_annotations('go', 'GO:2', 'genes') == set()
+        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()