diff get_data/kegg_glycan/test_findKEGG.py @ 1:0a5e0df17054 draft default tip

Uploaded

--- a/get_data/kegg_glycan/test_findKEGG.py	Wed Mar 23 14:35:56 2016 -0400
+++ b/get_data/kegg_glycan/test_findKEGG.py	Fri May 06 08:05:48 2016 -0400
@@ -41,9 +41,10 @@
             m = fk.find_entries_in_KEGG("john", "glucose")
 
     def test_unfindable_entry(self):
-        """should return None"""
+        """should return an empty string"""
         m = fk.find_entries_in_KEGG("glycan", "sally")
-        self.assertIsNone(m)
+        emptystring=""
+        self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
 
     def test_find_example(self):
         m = fk.find_entries_in_KEGG("glycan", "glucose")
@@ -52,9 +53,123 @@
 
     def test_query_has_newlines(self):
         """
-        should be fine and return entries
+        Assume a new line query is an AND query. 
+        """
+        m = fk.find_entries_in_KEGG("glycan", "glucose\nUDP")
+        self.assertIsNotNone(m)
+        print m
+        self.assertIn("UDP-D-glucose", m)
+
+    def test_query_has_newlines_and_a_space(self):
+        """
+        glucose\\n UDP. OR's should pass 
         """
         m = fk.find_entries_in_KEGG("glycan", "glucose\n UDP")
         self.assertIsNotNone(m)
         self.assertIn("UDP-D-glucose", m)
 
+    def test_gene_specific_or(self):
+        """
+        test "shiga toxin" returns. 
+         /find/genes/"shiga toxin" for keywords "shiga toxin"
+        """
+        m = fk.find_entries_in_KEGG("genes","shiga toxin")
+        self.assertIsNotNone(m)
+        #. not matching to all entries - that is silly, the db get updated!
+        self.assertIn("shiga", m)
+        self.assertIn("toxin", m)
+        self.assertNotIn("stm:STM0284",m) # should not be found in the OR query
+
+    def test_gene_specific_and(self):
+        """
+        test "shiga+toxin" returns. it should
+         /find/genes/shiga+toxin  	for keywords "shiga" and "toxin"
+        """
+        m = fk.find_entries_in_KEGG("genes","shiga+toxin")
+        self.assertIsNotNone(m)
+        #. not matching to all entries - that is silly, the db get updated!
+        self.assertIn("shiga", m)
+        self.assertIn("toxin", m)
+        self.assertIn("stm:STM0284",m) # should be found in the AND query
+
+    def test_enzyme_specific_1(self):
+        """
+        test 2.4.99.1 returns
+        """
+        m = fk.find_entries_in_KEGG("enzyme","2.4.99.1")
+        self.assertIsNotNone(m)
+        #. not matching to all entries - that is silly, the db get updated!
+        self.assertIn("2.4.99.1", m)
+
+    def test_enzyme_specific_2(self):
+        """
+        test 2.4.99.6 returns
+        """
+        m = fk.find_entries_in_KEGG("enzyme","2.4.99.6")
+        self.assertIsNotNone(m)
+        #. not matching to all entries - that is silly, the db get updated!
+        self.assertIn("2.4.99.6", m)
+
+    def test_enzyme_specific_3(self):
+        """
+        test ec: 2.4.99.6 with space (tests stripping space functionality)
+        """
+        m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.6")
+        self.assertIsNotNone(m)
+        #. not matching to all entries - that is silly, the db get updated!
+        self.assertIn("2.4.99.6", m)
+
+    def test_enzyme_specific_4(self):
+        """
+        test ec: 2.4.99. , should return 2.4.99.*
+        """
+        m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.")
+        self.assertIsNotNone(m)
+        #. not matching to all entries - that is silly, the db get updated!
+        self.assertIn("2.4.99.1", m)
+        self.assertIn("2.4.99.6", m)
+        self.assertIn("2.4.99.11", m)
+
+    def test_enzyme_specific_5(self):
+        """
+        test ec: 2.4.99.1+2.4.99.6 . AND function, so returns nothing here. Do not expect an enzyme to be doubly classified. 
+        """
+        m = fk.find_entries_in_KEGG("enzyme","2.4.99.1+2.4.99.6")
+        self.assertIsNotNone(m)
+        emptystring=""
+        self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
+
+    def test_enzyme_specific_6(self):
+        """
+        test ec: 2.4.99.1 2.4.99.6 . OR function, should return something but does not (KEGG FAILURE?).
+         note that trying this without "" will return the AND function result which is incorrect.
+        """
+        m = fk.find_entries_in_KEGG("enzyme","2.4.99.1 2.4.99.6")
+        self.assertIsNotNone(m)
+        #self.assertIn("2.4.99.1", m)
+        emptystring=""
+        print m
+        self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
+
+
+    def test_enzyme_specific_7(self):
+        """
+        test deoxy+1.1.1. . AND function, that should return something
+        """
+        m = fk.find_entries_in_KEGG("enzyme","deoxy+1.1.1")
+        self.assertIsNotNone(m)
+        print m
+        self.assertIn("deoxy", m)
+        self.assertIn("1.1.1", m)
+
+    def test_enzyme_specific_8(self):
+        """
+        test deoxy 1.1.1. . OR function. should return deoxy or 1.1.1. but does not (KEGG FAILURE?). i
+         note that trying this without "" will return the AND function result which is incorrect.
+        """
+        m = fk.find_entries_in_KEGG("enzyme","deoxy 1.1.1")
+        self.assertIsNotNone(m)
+        emptystring=""
+        print m
+        self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry")
+