Merge pull request #1058 from guzman-raphael/bug-activate

Schema activate ignores `create_tables=False`

Author: dimitri-yatsenko

CHANGELOG.md

@@ -1,5 +1,8 @@
 ## Release notes
 
+### 0.14.0 -- TBA
+* Bugfix - Activating a schema requires all tables to exist even if `create_tables=False` PR [#1058](https://github.com/datajoint/datajoint-python/pull/1058)
+
 ### 0.13.8 -- Sep 21, 2022
 * Add - New documentation structure based on markdown PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)
 * Bugfix - Fix queries with backslashes ([#999](https://github.com/datajoint/datajoint-python/issues/999)) PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)

datajoint/schemas.py

@@ -47,7 +47,7 @@ def __init__(
         connection=None,
         create_schema=True,
         create_tables=True,
-        add_objects=None
+        add_objects=None,
     ):
         """
         Associate database schema `schema_name`. If the schema does not exist, attempt to
@@ -87,7 +87,7 @@ def activate(
         connection=None,
         create_schema=None,
         create_tables=None,
-        add_objects=None
+        add_objects=None,
     ):
         """
         Associate database schema `schema_name`. If the schema does not exist, attempt to
@@ -222,9 +222,7 @@ def _decorate_table(self, table_class, context, assert_declared=False):
         # instantiate the class, declare the table if not already
         instance = table_class()
         is_declared = instance.is_declared
-        if not is_declared:
-            if not self.create_tables or assert_declared:
-                raise DataJointError("Table `%s` not declared" % instance.table_name)
+        if not is_declared and not assert_declared and self.create_tables:
             instance.declare(context)
             self.connection.dependencies.clear()
         is_declared = is_declared or instance.is_declared
@@ -506,7 +504,7 @@ def __init__(
         create_schema=False,
         create_tables=False,
         connection=None,
-        add_objects=None
+        add_objects=None,
     ):
         """
         Creates a python module with the given name from the name of a schema on the server and

datajoint/version.py

@@ -1,3 +1,3 @@
-__version__ = "0.13.8"
+__version__ = "0.14.0"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters

local-docker-compose.yml

@@ -95,6 +95,7 @@ services:
         ## Interactive Jupyter Notebook environment
         jupyter notebook &
         ## Remote debugger
+        set +e
         while true
         do
           python -m ptvsd --host 0.0.0.0 --port 5678 --wait .

tests/schema_privileges.py

@@ -0,0 +1,35 @@
+import datajoint as dj
+
+schema = dj.Schema()
+
+
+@schema
+class Parent(dj.Lookup):
+    definition = """
+    id: int
+    """
+    contents = [(1,)]
+
+
+@schema
+class Child(dj.Computed):
+    definition = """
+    -> Parent
+    """
+
+    def make(self, key):
+        self.insert1(key)
+
+
+@schema
+class NoAccess(dj.Lookup):
+    definition = """
+    string: varchar(10)
+    """
+
+
+@schema
+class NoAccessAgain(dj.Manual):
+    definition = """
+    -> NoAccess
+    """

tests/test_blob.py

@@ -230,7 +230,7 @@ def test_insert_longblob():
 
 def test_datetime_serialization_speed():
     # If this fails that means for some reason deserializing/serializing
-    # np arrays of np.datetime64 types is now slower than regular arrays of datetime64
+    # np arrays of np.datetime64 types is now slower than regular arrays of datetime
 
     optimized_exe_time = timeit.timeit(
         setup="myarr=pack(np.array([np.datetime64('2022-10-13 03:03:13') for _ in range(0, 10000)]))",
@@ -247,4 +247,4 @@ def test_datetime_serialization_speed():
     )
     print(f"python time {baseline_exe_time}")
 
-    assert optimized_exe_time * 1000 < baseline_exe_time
+    assert optimized_exe_time * 900 < baseline_exe_time

tests/test_privileges.py

@@ -1,6 +1,8 @@
-from nose.tools import assert_true, raises
+import importlib
 import datajoint as dj
-from . import schema, CONN_INFO
+from . import schema, CONN_INFO_ROOT, PREFIX
+from . import schema_privileges as pipeline
+from nose.tools import assert_true, raises
 
 namespace = locals()
 
@@ -10,7 +12,7 @@ class TestUnprivileged:
     def setup_class(cls):
         """A connection with only SELECT privilege to djtest schemas"""
         cls.connection = dj.conn(
-            host=CONN_INFO["host"], user="djview", password="djview", reset=True
+            host=CONN_INFO_ROOT["host"], user="djview", password="djview", reset=True
         )
 
     @raises(dj.DataJointError)
@@ -46,3 +48,62 @@ class Try(dj.Manual):
             """
 
         Try().insert1((1, 1.5))
+
+
+class TestSubset:
+    USER = "djsubset"
+
+    @classmethod
+    def setup_class(cls):
+        conn = dj.conn(
+            host=CONN_INFO_ROOT["host"],
+            user=CONN_INFO_ROOT["user"],
+            password=CONN_INFO_ROOT["password"],
+            reset=True,
+        )
+        pipeline.schema.activate(f"{PREFIX}_pipeline")
+        conn.query(
+            f"""
+            CREATE USER IF NOT EXISTS '{cls.USER}'@'%%'
+            IDENTIFIED BY '{cls.USER}'
+            """
+        )
+        conn.query(
+            f"""
+            GRANT SELECT, INSERT, UPDATE, DELETE
+            ON `{PREFIX}_pipeline`.`#parent`
+            TO '{cls.USER}'@'%%'
+            """
+        )
+        conn.query(
+            f"""
+            GRANT SELECT, INSERT, UPDATE, DELETE
+            ON `{PREFIX}_pipeline`.`__child`
+            TO '{cls.USER}'@'%%'
+            """
+        )
+        cls.connection = dj.conn(
+            host=CONN_INFO_ROOT["host"],
+            user=cls.USER,
+            password=cls.USER,
+            reset=True,
+        )
+
+    @classmethod
+    def teardown_class(cls):
+        conn = dj.conn(
+            host=CONN_INFO_ROOT["host"],
+            user=CONN_INFO_ROOT["user"],
+            password=CONN_INFO_ROOT["password"],
+            reset=True,
+        )
+        conn.query(f"DROP USER {cls.USER}")
+        conn.query(f"DROP DATABASE {PREFIX}_pipeline")
+
+    def test_populate_activate(self):
+        importlib.reload(pipeline)
+        pipeline.schema.activate(
+            f"{PREFIX}_pipeline", create_schema=True, create_tables=False
+        )
+        pipeline.Child.populate()
+        assert pipeline.Child.progress(display=False)[0] == 0