simplify context management, move test initialization into setup_class from __init__ in nosetests

Author: dimitri-yatsenko

datajoint/declare.py

@@ -194,7 +194,7 @@ def declare(full_table_name, definition, context):
 
     :param full_table_name: full name of the table
     :param definition: DataJoint table definition
-    :param context: dictionary of objects that might be referred to in the table. Usually this will be locals()
+    :param context: dictionary of objects that might be referred to in the table.
     """
     # split definition into lines
     definition = re.split(r'\s*\n\s*', definition.strip())

datajoint/schema.py

@@ -218,15 +218,14 @@ def process_relation_class(self, relation_class, context, assert_declared=False)
         relation_class.database = self.database
         relation_class._connection = self.connection
         relation_class._heading = Heading()
-        relation_class._context = context
         # instantiate the class, declare the table if not already
         instance = relation_class()
         is_declared = instance.is_declared
         if not is_declared:
             if not self.create_tables or assert_declared:
                 raise DataJointError('Table not declared %s' % instance.table_name)
             else:
-                instance.declare()
+                instance.declare(context)
         is_declared = is_declared or instance.is_declared
 
         # fill values in Lookup tables from their contents property

datajoint/table.py

@@ -28,11 +28,10 @@ class Table(QueryExpression):
     """
     Table is an abstract class that represents a base relation, i.e. a table in the schema.
     To make it a concrete class, override the abstract properties specifying the connection,
-    table name, database, context, and definition.
+    table name, database, and definition.
     A Relation implements insert and delete methods in addition to inherited relational operators.
     """
     _heading = None
-    _context = None
     database = None
     _log_ = None
     _external_table = None
@@ -55,16 +54,12 @@ def heading(self):
                 self._heading.init_from_database(self.connection, self.database, self.table_name)
         return self._heading
 
-    @property
-    def context(self):
-        return self._context
-
-    def declare(self):
+    def declare(self, context=None):
         """
         Use self.definition to declare the table in the schema.
         """
         try:
-            sql, uses_external = declare(self.full_table_name, self.definition, self._context)
+            sql, uses_external = declare(self.full_table_name, self.definition, context)
             if uses_external:
                 # trigger the creation of the external hash lookup for the current schema
                 external_table = self.connection.schemas[self.database].external_table

datajoint/user_tables.py

@@ -65,7 +65,6 @@ class UserTable(Table, metaclass=OrderedClass):
     UserTable is initialized by the decorator generated by schema().
     """
     _connection = None
-    _context = None
     _heading = None
     tier_regexp = None
     _prefix = None
@@ -143,7 +142,6 @@ class Part(UserTable):
     """
 
     _connection = None
-    _context = None
     _heading = None
     _master = None
 

tests/__init__.py

@@ -6,7 +6,7 @@
 """
 
 import logging
-from os import environ
+from os import environ, remove
 import datajoint as dj
 
 __author__ = 'Edgar Walker, Fabian Sinz, Dimitri Yatsenko'
@@ -47,3 +47,4 @@ def teardown_package():
     for db in cur.fetchall():
         conn.query('DROP DATABASE `{}`'.format(db[0]))
     conn.query('SET FOREIGN_KEY_CHECKS=1')
+    remove("dj_local_conf.json")

tests/schema.py

@@ -12,7 +12,7 @@
 
 
 @schema
-class Test(dj.Lookup):
+class TTest(dj.Lookup):
     definition = """
     key   :   int     # key
     ---
@@ -22,7 +22,7 @@ class Test(dj.Lookup):
 
 
 @schema
-class Test2(dj.Manual):
+class TTest2(dj.Manual):
     definition = """
     key   :   int     # key
     ---
@@ -31,7 +31,7 @@ class Test2(dj.Manual):
 
 
 @schema
-class Test3(dj.Manual):
+class TTest3(dj.Manual):
     definition = """
     key : int 
     ---
@@ -40,19 +40,19 @@ class Test3(dj.Manual):
 
 
 @schema
-class TestExtra(dj.Manual):
+class TTestExtra(dj.Manual):
     """
     clone of Test but with an extra field
     """
-    definition = Test.definition + "\nextra : int # extra int\n"
+    definition = TTest.definition + "\nextra : int # extra int\n"
 
 
 @schema
-class TestNoExtra(dj.Manual):
+class TTestNoExtra(dj.Manual):
     """
     clone of Test but with no extra fields
     """
-    definition = Test.definition
+    definition = TTest.definition
 
 
 @schema

tests/schema_simple.py

@@ -143,7 +143,7 @@ class DataB(dj.Lookup):
 
 
 @schema
-class TestUpdate(dj.Lookup):
+class TTestUpdate(dj.Lookup):
     definition = """
     primary_key     : int
     ---

tests/test_blob2.py

@@ -1,6 +1,7 @@
 import numpy as np
+import os
 import datajoint as dj
-from nose.tools import assert_equal, assert_true, assert_list_equal, assert_tuple_equal
+from nose.tools import assert_equal, assert_true, assert_list_equal, assert_tuple_equal, assert_false
 
 from . import PREFIX, CONN_INFO
 
@@ -49,7 +50,10 @@ def insert_blobs():
 
 
 class TestFetch:
-    def __init__(self):
+
+    @classmethod
+    def setup_class(cls):
+        assert_false(dj.config['safemode'], 'safemode must be disabled')
         Blob().delete()
         insert_blobs()
 

tests/test_connection.py

@@ -55,9 +55,10 @@ class Subjects(dj.Manual):
         species = "mouse"           : enum('mouse', 'monkey', 'human')   # species
         """
 
-    def __init__(self):
-        self.relation = self.Subjects()
-        self.conn = dj.conn(**CONN_INFO)
+    @classmethod
+    def setup_class(cls):
+        cls.relation = cls.Subjects()
+        cls.conn = dj.conn(**CONN_INFO)
 
     def teardown(self):
         self.relation.delete_quick()

tests/test_fetch.py

@@ -10,9 +10,10 @@
 
 class TestFetch:
 
-    def __init__(self):
-        self.subject = schema.Subject()
-        self.lang = schema.Language()
+    @classmethod
+    def setup_class(cls):
+        cls.subject = schema.Subject()
+        cls.lang = schema.Language()
 
     def test_getattribute(self):
         """Testing Fetch.__call__ with attributes"""

tests/test_nan.py

@@ -16,13 +16,14 @@ class NanTest(dj.Manual):
 
 
 class TestNaNInsert:
-    def __init__(self):
-        self.rel = NanTest()
+    @classmethod
+    def setup_class(cls):
+        cls.rel = NanTest()
         with dj.config(safemode=False):
-            self.rel.delete()
+            cls.rel.delete()
         a = np.array([0, 1/3, np.nan, np.pi, np.nan])
-        self.rel.insert(((i, value) for i, value in enumerate(a)))
-        self.a = a
+        cls.rel.insert(((i, value) for i, value in enumerate(a)))
+        cls.a = a
 
     def test_insert_nan(self):
         """Test fetching of null values"""

tests/test_privileges.py

@@ -8,9 +8,10 @@
 
 class TestUnprivileged:
 
-    def __init__(self):
+    @classmethod
+    def setup_class(cls):
         """A connection with only SELECT privilege to djtest schemas"""
-        self.connection = dj.Connection(host=environ.get('DJ_TEST_HOST', 'localhost'), user='djview', password='djview')
+        cls.connection = dj.Connection(host=environ.get('DJ_TEST_HOST', 'localhost'), user='djview', password='djview')
 
     @raises(dj.DataJointError)
     def test_fail_create_schema(self):

tests/test_relation.py

@@ -24,24 +24,24 @@ class TestRelation:
     Test base relations: insert, delete
     """
 
-    def __init__(self):
-        self.test = schema.Test()
-        self.test_extra = schema.TestExtra()
-        self.test_no_extra = schema.TestNoExtra()
-        self.user = schema.User()
-        self.subject = schema.Subject()
-        self.experiment = schema.Experiment()
-        self.trial = schema.Trial()
-        self.ephys = schema.Ephys()
-        self.channel = schema.Ephys.Channel()
-        self.img = schema.Image()
-        self.trash = schema.UberTrash()
+    @classmethod
+    def setup_class(cls):
+        cls.test = schema.TTest()
+        cls.test_extra = schema.TTestExtra()
+        cls.test_no_extra = schema.TTestNoExtra()
+        cls.user = schema.User()
+        cls.subject = schema.Subject()
+        cls.experiment = schema.Experiment()
+        cls.trial = schema.Trial()
+        cls.ephys = schema.Ephys()
+        cls.channel = schema.Ephys.Channel()
+        cls.img = schema.Image()
+        cls.trash = schema.UberTrash()
 
     def test_contents(self):
         """
         test the ability of tables to self-populate using the contents property
         """
-
         # test contents
         assert_true(self.user)
         assert_true(len(self.user) == len(self.user.contents))
@@ -96,9 +96,9 @@ def test_wrong_insert_type(self):
         self.user.insert1(3)
 
     def test_insert_select(self):
-        schema.Test2.delete()
-        schema.Test2.insert(schema.Test)
-        assert_equal(len(schema.Test2()), len(schema.Test()))
+        schema.TTest2.delete()
+        schema.TTest2.insert(schema.TTest)
+        assert_equal(len(schema.TTest2()), len(schema.TTest()))
         original_length = len(self.subject)
         self.subject.insert(self.subject.proj(
             'real_id', 'date_of_birth', 'subject_notes', subject_id='subject_id+1000', species='"human"'))
@@ -205,9 +205,13 @@ def test_blob_insert(self):
     def test_drop(self):
         """Tests dropping tables"""
         dj.config['safemode'] = True
-        with patch.object(utils, "input", create=True, return_value='yes'):
-            self.trash.drop()
-        dj.config['safemode'] = False
+        try:
+            with patch.object(utils, "input", create=True, return_value='yes'):
+                self.trash.drop()
+        except:
+            pass
+        finally:
+            dj.config['safemode'] = False
         self.trash.fetch()
 
     def test_table_regexp(self):

tests/test_relation_u.py

@@ -8,16 +8,17 @@ class TestU:
     Test base relations: insert, delete
     """
 
-    def __init__(self):
-        self.user = schema.User()
-        self.language = schema.Language()
-        self.subject = schema.Subject()
-        self.experiment = schema.Experiment()
-        self.trial = schema.Trial()
-        self.ephys = schema.Ephys()
-        self.channel = schema.Ephys.Channel()
-        self.img = schema.Image()
-        self.trash = schema.UberTrash()
+    @classmethod
+    def setup_class(cls):
+        cls.user = schema.User()
+        cls.language = schema.Language()
+        cls.subject = schema.Subject()
+        cls.experiment = schema.Experiment()
+        cls.trial = schema.Trial()
+        cls.ephys = schema.Ephys()
+        cls.channel = schema.Ephys.Channel()
+        cls.img = schema.Image()
+        cls.trash = schema.UberTrash()
 
     def test_restriction(self):
         language_set = {s[1] for s in self.language.contents}
@@ -60,7 +61,7 @@ def test_aggregations(self):
         assert_equal((rel & 'language="English"').fetch1('number_of_speakers'), 3)
 
     def test_argmax(self):
-        rel = schema.Test()
+        rel = schema.TTest()
         # get the tuples corresponding to maximum value
         mx = (rel * dj.U().aggr(rel, mx='max(value)')) & 'mx=value'
         assert_equal(mx.fetch('value')[0], max(rel.fetch('value')))