Python DictList.query方法代码示例

# 需要导入模块: from cobra import DictList [as 别名]
# 或者: from cobra.DictList import query [as 别名]
class TestDictList(TestCase):
    def setUp(self):
        self.obj = Object("test1")
        self.list = DictList()
        self.list.append(self.obj)

    def testAppend(self):
        obj2 = Object("test2")
        self.list.append(obj2)
        self.assertRaises(ValueError, self.list.append,
            Object("test1"))
        self.assertEqual(self.list.index(obj2), 1)
        self.assertEqual(self.list[1], obj2)
        self.assertEqual(self.list.get_by_id("test2"), obj2)
        self.assertEqual(len(self.list), 2)

    def testExtend(self):
        obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
        self.list.extend(obj_list)
        self.assertEqual(self.list[1].id, "test2")
        self.assertEqual(self.list.get_by_id("test2"), obj_list[0])
        self.assertEqual(self.list[8].id, "test9")
        self.assertEqual(len(self.list), 9)

    def testIadd(self):
        obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
        self.list += obj_list
        self.assertEqual(self.list[1].id, "test2")
        self.assertEqual(self.list.get_by_id("test2"), obj_list[0])
        self.assertEqual(self.list[8].id, "test9")
        self.assertEqual(len(self.list), 9)


    def testAdd(self):
        obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
        sum = self.list + obj_list
        self.assertEqual(self.list[0].id, "test1")
        self.assertEqual(sum[1].id, "test2")
        self.assertEqual(sum.get_by_id("test2"), obj_list[0])
        self.assertEqual(sum[8].id, "test9")
        self.assertEqual(len(self.list), 1)
        self.assertEqual(len(sum), 9)

    def testDeepcopy(self):
        from copy import deepcopy
        copied = deepcopy(self.list)
        for i, v in enumerate(self.list):
            assert self.list[i].id == copied[i].id
            assert self.list[i] is not copied[i]

    def testQuery(self):
        obj2 = Object("test2")
        self.list.append(obj2)
        result = self.list.query("test1")  # matches only test1
        self.assertEqual(len(result), 1)
        self.assertEqual(result[0], self.obj)
        result = self.list.query("test")  # matches test1 and test2
        self.assertEqual(len(result), 2)

# 需要导入模块: from cobra import DictList [as 别名]
# 或者: from cobra.DictList import query [as 别名]

#.........这里部分代码省略.........
            self.assertIs(self.list[i], copied[i])
            self.assertIs(v, copied.get_by_id(v.id))

    def testDeepcopy(self):
        self.list.append(Object("test2"))
        copied = deepcopy(self.list)
        self.assertIsNot(self.list, copied)
        self.assertIsInstance(copied, self.list.__class__)
        self.assertEqual(len(self.list), len(copied))
        for i, v in enumerate(self.list):
            self.assertEqual(self.list[i].id, copied[i].id)
            self.assertEqual(i, copied.index(v.id))
            self.assertIsNot(self.list[i], copied[i])
            self.assertIsNot(v, copied.get_by_id(v.id))

    def testPickle(self):
        self.list.append(Object("test2"))
        for protocol in range(HIGHEST_PROTOCOL):
            pickle_str = dumps(self.list, protocol=protocol)
            copied = loads(pickle_str)
            self.assertIsNot(self.list, copied)
            self.assertIsInstance(copied, self.list.__class__)
            self.assertEqual(len(self.list), len(copied))
            for i, v in enumerate(self.list):
                self.assertEqual(self.list[i].id, copied[i].id)
                self.assertEqual(i, copied.index(v.id))
                self.assertIsNot(self.list[i], copied[i])
                self.assertIsNot(v, copied.get_by_id(v.id))

    def testQuery(self):
        obj2 = Object("test2")
        obj2.name = "foobar1"
        self.list.append(obj2)
        result = self.list.query("test1")  # matches only test1
        self.assertEqual(len(result), 1)
        self.assertEqual(result[0], self.obj)
        result = self.list.query("foo", "name")  # matches only test2
        self.assertEqual(len(result), 1)
        self.assertEqual(result[0], obj2)
        result = self.list.query("test")  # matches test1 and test2
        self.assertEqual(len(result), 2)
        # test with a regular expression
        result = self.list.query(re.compile("test[0-9]"))
        self.assertEqual(len(result), 2)
        result = self.list.query(re.compile("test[29]"))
        self.assertEqual(len(result), 1)
        # test query of name
        result = self.list.query(re.compile("foobar."), "name")
        self.assertEqual(len(result), 1)

    def testRemoval(self):
        obj_list = DictList(Object("test%d" % (i)) for i in range(2, 10))
        del obj_list[3]
        self.assertNotIn("test5", obj_list)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        self.assertEqual(len(obj_list), 7)
        del obj_list[3:5]
        self.assertNotIn("test6", obj_list)
        self.assertNotIn("test7", obj_list)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        self.assertEqual(len(obj_list), 5)
        removed = obj_list.pop(1)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        self.assertEqual(removed.id, "test3")
        self.assertNotIn("test3", obj_list)
        self.assertEqual(len(obj_list), 4)

# 需要导入模块: from cobra import DictList [as 别名]
# 或者: from cobra.DictList import query [as 别名]

#.........这里部分代码省略.........
    def testInitCopy(self):
        self.list.append(Object("test2"))
        copied = DictList(self.list)
        self.assertIsNot(self.list, copied)
        self.assertIsInstance(copied, self.list.__class__)
        self.assertEqual(len(self.list), len(copied))
        for i, v in enumerate(self.list):
            self.assertEqual(self.list[i].id, copied[i].id)
            self.assertEqual(i, copied.index(v.id))
            self.assertIs(self.list[i], copied[i])
            self.assertIs(v, copied.get_by_id(v.id))

    def testSlice(self):
        self.list.append(Object("test2"))
        self.list.append(Object("test3"))
        sliced = self.list[:-1]
        self.assertIsNot(self.list, sliced)
        self.assertIsInstance(sliced, self.list.__class__)
        self.assertEqual(len(self.list), len(sliced) + 1)
        for i, v in enumerate(sliced):
            self.assertEqual(self.list[i].id, sliced[i].id)
            self.assertEqual(i, sliced.index(v.id))
            self.assertIs(self.list[i], sliced[i])
            self.assertIs(self.list[i], sliced.get_by_id(v.id))

    def testCopy(self):
        self.list.append(Object("test2"))
        copied = copy(self.list)
        self.assertIsNot(self.list, copied)
        self.assertIsInstance(copied, self.list.__class__)
        self.assertEqual(len(self.list), len(copied))
        for i, v in enumerate(self.list):
            self.assertEqual(self.list[i].id, copied[i].id)
            self.assertEqual(i, copied.index(v.id))
            self.assertIs(self.list[i], copied[i])
            self.assertIs(v, copied.get_by_id(v.id))

    def testDeepcopy(self):
        self.list.append(Object("test2"))
        copied = deepcopy(self.list)
        self.assertIsNot(self.list, copied)
        self.assertIsInstance(copied, self.list.__class__)
        self.assertEqual(len(self.list), len(copied))
        for i, v in enumerate(self.list):
            self.assertEqual(self.list[i].id, copied[i].id)
            self.assertEqual(i, copied.index(v.id))
            self.assertIsNot(self.list[i], copied[i])
            self.assertIsNot(v, copied.get_by_id(v.id))

    def testPickle(self):
        self.list.append(Object("test2"))
        for protocol in range(HIGHEST_PROTOCOL):
            pickle_str = dumps(self.list, protocol=protocol)
            copied = loads(pickle_str)
            self.assertIsNot(self.list, copied)
            self.assertIsInstance(copied, self.list.__class__)
            self.assertEqual(len(self.list), len(copied))
            for i, v in enumerate(self.list):
                self.assertEqual(self.list[i].id, copied[i].id)
                self.assertEqual(i, copied.index(v.id))
                self.assertIsNot(self.list[i], copied[i])
                self.assertIsNot(v, copied.get_by_id(v.id))

    def testQuery(self):
        obj2 = Object("test2")
        self.list.append(obj2)
        result = self.list.query("test1")  # matches only test1
        self.assertEqual(len(result), 1)
        self.assertEqual(result[0], self.obj)
        result = self.list.query("test")  # matches test1 and test2
        self.assertEqual(len(result), 2)

    def testRemoval(self):
        obj_list = DictList(Object("test%d" % (i)) for i in range(2, 10))
        del obj_list[3]
        self.assertNotIn("test5", obj_list)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        del obj_list[3:5]
        self.assertNotIn("test6", obj_list)
        self.assertNotIn("test7", obj_list)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        removed = obj_list.pop(1)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        self.assertEqual(removed.id, "test3")
        self.assertNotIn("test3", obj_list)

    def testSet(self):
        obj_list = DictList(Object("test%d" % (i)) for i in range(10))
        obj_list[4] = Object("testa")
        self.assertEqual(obj_list.index("testa"), 4)
        self.assertEqual(obj_list[4].id, "testa")
        obj_list[5:7] = [Object("testb"), Object("testc")]
        self.assertEqual(obj_list.index("testb"), 5)
        self.assertEqual(obj_list[5].id, "testb")
        self.assertEqual(obj_list.index("testc"), 6)
        self.assertEqual(obj_list[6].id, "testc")
        # Even if the object is unique, if it is present twice in the new
        # list, it should still raise an exception
        self.assertRaises(ValueError, obj_list.__setitem__, slice(5, 7),
                          [Object("testd"), Object("testd")])

# 需要导入模块: from cobra import DictList [as 别名]
# 或者: from cobra.DictList import query [as 别名]
class TestDictList(TestCase):
    def setUp(self):
        self.obj = Object("test1")
        self.list = DictList()
        self.list.append(self.obj)

    def testIndependent(self):
        a = DictList([Object("o1"), Object("o2")])
        b = DictList()
        self.assertIn("o1", a)
        self.assertNotIn("o1", b)
        b.append(Object("o3"))
        self.assertNotIn("o3", a)
        self.assertIn("o3", b)

    def testAppend(self):
        obj2 = Object("test2")
        self.list.append(obj2)
        self.assertRaises(ValueError, self.list.append,
            Object("test1"))
        self.assertEqual(self.list.index(obj2), 1)
        self.assertEqual(self.list[1], obj2)
        self.assertEqual(self.list.get_by_id("test2"), obj2)
        self.assertEqual(len(self.list), 2)

    def testExtend(self):
        obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
        self.list.extend(obj_list)
        self.assertEqual(self.list[1].id, "test2")
        self.assertEqual(self.list.get_by_id("test2"), obj_list[0])
        self.assertEqual(self.list[8].id, "test9")
        self.assertEqual(len(self.list), 9)

    def testIadd(self):
        obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
        self.list += obj_list
        self.assertEqual(self.list[1].id, "test2")
        self.assertEqual(self.list.get_by_id("test2"), obj_list[0])
        self.assertEqual(self.list[8].id, "test9")
        self.assertEqual(len(self.list), 9)


    def testAdd(self):
        obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
        sum = self.list + obj_list
        self.assertEqual(self.list[0].id, "test1")
        self.assertEqual(sum[1].id, "test2")
        self.assertEqual(sum.get_by_id("test2"), obj_list[0])
        self.assertEqual(sum[8].id, "test9")
        self.assertEqual(len(self.list), 1)
        self.assertEqual(len(sum), 9)

    def testDeepcopy(self):
        from copy import deepcopy
        copied = deepcopy(self.list)
        for i, v in enumerate(self.list):
            self.assertEqual(self.list[i].id, copied[i].id)
            self.assertIsNot(self.list[i], copied[i])

    def testQuery(self):
        obj2 = Object("test2")
        self.list.append(obj2)
        result = self.list.query("test1")  # matches only test1
        self.assertEqual(len(result), 1)
        self.assertEqual(result[0], self.obj) 
        result = self.list.query("test")  # matches test1 and test2
        self.assertEqual(len(result), 2)

    def testRemoval(self):
        obj_list = DictList(Object("test%d" % (i)) for i in range(2, 10))
        del obj_list[3]
        self.assertNotIn("test5", obj_list)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        del obj_list[3:5]
        self.assertNotIn("test6", obj_list)
        self.assertNotIn("test7", obj_list)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        removed = obj_list.pop(1)
        self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
        self.assertEqual(removed.id, "test3")
        self.assertNotIn("test3", obj_list)

    def testSet(self):
        obj_list = DictList(Object("test%d" % (i)) for i in range(10))
        obj_list[4] = Object("testa")
        self.assertEqual(obj_list.index("testa"), 4)
        self.assertEqual(obj_list[4].id, "testa")
        obj_list[5:7] = [Object("testb"), Object("testc")]
        self.assertEqual(obj_list.index("testb"), 5)
        self.assertEqual(obj_list[5].id, "testb")
        self.assertEqual(obj_list.index("testc"), 6)
        self.assertEqual(obj_list[6].id, "testc")

# 需要导入模块: from cobra import DictList [as 别名]
# 或者: from cobra.DictList import query [as 别名]

#.........这里部分代码省略.........
        lb = self.construct_attribute_vector("lower_bound", solution.f)
        ub = self.construct_attribute_vector("upper_bound", solution.f)
        x = array(solution.x)
        err = abs(S * x)
        errors["max_error"] = err.max()
        errors["sum_error"] = err.sum()
        ub_err = min(ub - x)
        errors["upper_bound_error"] = abs(ub_err) if ub_err < 0 else 0
        lb_err = min(x - lb)
        errors["lower_bound_error"] = abs(lb_err) if lb_err < 0 else 0
        return errors

    def update(self):
        """updates all component reactions"""
        for r in self.reactions:
            if hasattr(r, "update"):
                r.update()

    def prune(self):
        """remove all unused metabolites and reactions

        This should be run after the model is fully built. It will be
        difficult to add new content to the model once this has been run.

        """
        complex_data_list = [i.id for i in self.complex_data]
        for c_d in complex_data_list:
            c = self.complex_data.get_by_id(c_d)
            cplx = c.complex
            if len(cplx.reactions) == 1:
                list(cplx.reactions)[0].delete(remove_orphans=True)
                self.complex_data.remove(self.complex_data.get_by_id(c_d))

        for p in self.metabolites.query(re.compile('^protein_')):
            if isinstance(p, ProcessedProtein):
                delete = True
                for rxn in p._reaction:
                    try:
                        if p in rxn.reactants:
                            delete = False
                    except Exception as e:
                        print(rxn)
                        raise e
                if delete:
                    while len(p._reaction) > 0:
                        list(p._reaction)[0].delete(remove_orphans=True)
                        for data in self.posttranslation_data.query(p.id):
                            self.posttranslation_data.remove(data.id)

        for p in self.metabolites.query(re.compile('^protein_')):
            if isinstance(p, TranslatedGene):
                delete = True
                for rxn in p._reaction:
                    try:
                        if p in rxn.reactants and not rxn.id.startswith('degradation'):
                            delete = False
                    except Exception as e:
                        print(rxn)
                        raise e
                if delete:
                    while len(p._reaction) > 0:
                        list(p._reaction)[0].delete(remove_orphans=True)
                        p_id = p.id.replace('protein_', '')
                        for data in self.translation_data.query(p_id):
                            self.translation_data.remove(data.id)