Merge pull request #732 from guzman-raphael/schema

Rename dj.schema to dj.Schema and dj.create_virtual_module to dj.VirtualModule

Author: dimitri-yatsenko

CHANGELOG.md

@@ -1,5 +1,12 @@
 ## Release notes
 
+### 0.12.5 -- Feb TBA, 2020
+* Rename module `dj.schema` into `dj.schemas`. `dj.schema` remains an alias for class `dj.Schema`. (#731) PR #732
+* `dj.create_virtual_module` is now called `dj.VirtualModule` (#731) PR #732
+* Bugfix - SSL `KeyError` on failed connection (#716) PR #725
+* Bugfix - Unable to run unit tests using nosetests (#723) PR #724
+* Bugfix - `suppress_errors` does not suppress loss of connection error (#720) PR #721
+
 ### 0.12.4 -- Jan 14, 2020
 * Support for simple scalar datatypes in blobs (#690) PR #709
 * Add support for the `serial` data type in declarations: alias for `bigint unsigned auto_increment` PR #713

LNX-docker-compose.yml

@@ -14,10 +14,10 @@ services:
       fakeservices.datajoint.io:
         condition: service_healthy
     environment:
-      - DJ_HOST=db
+      - DJ_HOST=fakeservices.datajoint.io
       - DJ_USER=root
       - DJ_PASS=simple
-      - DJ_TEST_HOST=db
+      - DJ_TEST_HOST=fakeservices.datajoint.io
       - DJ_TEST_USER=datajoint
       - DJ_TEST_PASSWORD=datajoint
       - S3_ENDPOINT=fakeservices.datajoint.io:9000
@@ -57,10 +57,10 @@ services:
     #   - ./mysql/data:/var/lib/mysql
   minio:
     <<: *net
+    image: minio/minio:$MINIO_VER
     environment:
       - MINIO_ACCESS_KEY=datajoint
       - MINIO_SECRET_KEY=datajoint
-    image: minio/minio:$MINIO_VER
     # ports:
     #   - "9000:9000"
     # volumes:
@@ -79,6 +79,7 @@ services:
       - URL=datajoint.io
       - SUBDOMAINS=fakeservices
       - MINIO_SERVER=http://minio:9000
+      - MYSQL_SERVER=db:3306
     entrypoint: /entrypoint.sh
     healthcheck:
       test: wget --quiet --tries=1 --spider https://fakeservices.datajoint.io:443/minio/health/live || exit 1
@@ -88,8 +89,10 @@ services:
     # ports:
     #   - "9000:9000"
     #   - "443:443"
+    #   - "3306:3306"
     volumes:
       - ./tests/nginx/base.conf:/base.conf
+      - ./tests/nginx/nginx.conf:/nginx.conf
       - ./tests/nginx/entrypoint.sh:/entrypoint.sh
       - ./tests/nginx/fullchain.pem:/certs/fullchain.pem
       - ./tests/nginx/privkey.pem:/certs/privkey.pem

datajoint/__init__.py

@@ -18,8 +18,8 @@
 __date__ = "February 7, 2019"
 __all__ = ['__author__', '__version__',
            'config', 'conn', 'Connection',
-           'schema', 'create_virtual_module', 'list_schemas',
-           'Table', 'FreeTable',
+           'Schema', 'schema', 'VirtualModule', 'create_virtual_module',
+           'list_schemas', 'Table', 'FreeTable',
            'Manual', 'Lookup', 'Imported', 'Computed', 'Part',
            'Not', 'AndList', 'U', 'Diagram', 'Di', 'ERD',
            'set_password', 'kill',
@@ -29,8 +29,8 @@
 from .version import __version__
 from .settings import config
 from .connection import conn, Connection
-from .schema import Schema as schema
-from .schema import create_virtual_module, list_schemas
+from .schemas import Schema
+from .schemas import VirtualModule, list_schemas
 from .table import Table, FreeTable
 from .user_tables import Manual, Lookup, Imported, Computed, Part
 from .expression import Not, AndList, U
@@ -43,4 +43,6 @@
 from .errors import DataJointError
 from .migrate import migrate_dj011_external_blob_storage_to_dj012
 
-ERD = Di = Diagram   # Aliases for Diagram
+ERD = Di = Diagram                      # Aliases for Diagram
+schema = Schema                         # Aliases for Schema
+create_virtual_module = VirtualModule   # Aliases for VirtualModule

datajoint/migrate.py

@@ -25,7 +25,7 @@ def migrate_dj011_external_blob_storage_to_dj012(migration_schema, store):
 Proceed?
             """, default='no') == 'yes'
     if do_migration:
-        _migrate_dj011_blob(dj.schema(migration_schema), store)
+        _migrate_dj011_blob(dj.Schema(migration_schema), store)
         print('Migration completed for schema: {}, store: {}.'.format(
                 migration_schema, store))
         return

datajoint/schema.py renamed to datajoint/schemas.py

@@ -280,8 +280,8 @@ def repl(s):
         body = '\n\n\n'.join(make_class_definition(table) for table in diagram.topological_sort())
         python_code = '\n\n\n'.join((
             '"""This module was auto-generated by datajoint from an existing schema"""',
-            "import datajoint as dj\n\nschema = dj.schema('{db}')".format(db=db),
-            '\n'.join("{module} = dj.create_virtual_module('{module}', '{schema_name}')".format(module=v, schema_name=k)
+            "import datajoint as dj\n\nschema = dj.Schema('{db}')".format(db=db),
+            '\n'.join("{module} = dj.VirtualModule('{module}', '{schema_name}')".format(module=v, schema_name=k)
                       for k, v in module_lookup.items()), body))
         if python_filename is None:
             return python_code
@@ -290,26 +290,30 @@ def repl(s):
                 f.write(python_code)
 
 
-def create_virtual_module(module_name, schema_name, *,
-                          create_schema=False, create_tables=False, connection=None, add_objects=None):
+class VirtualModule(types.ModuleType):
     """
-    Creates a python module with the given name from the name of a schema on the server and
-    automatically adds classes to it corresponding to the tables in the schema.
-    :param module_name: displayed module name
-    :param schema_name: name of the database in mysql
-    :param create_schema: if True, create the schema on the database server
-    :param create_tables: if True, module.schema can be used as the decorator for declaring new
-    :param connection: a dj.Connection object to pass into the schema
-    :param add_objects: additional objects to add to the module
-    :return: the python module containing classes from the schema object and the table classes
+    A virtual module which will contain context for schema.
     """
-    module = types.ModuleType(module_name)
-    _schema = Schema(schema_name, create_schema=create_schema, create_tables=create_tables, connection=connection)
-    if add_objects:
-        module.__dict__.update(add_objects)
-    module.__dict__['schema'] = _schema
-    _schema.spawn_missing_classes(context=module.__dict__)
-    return module
+    def __init__(self, module_name, schema_name, *, create_schema=False, 
+                    create_tables=False, connection=None, add_objects=None):
+        """
+        Creates a python module with the given name from the name of a schema on the server and
+        automatically adds classes to it corresponding to the tables in the schema.
+        :param module_name: displayed module name
+        :param schema_name: name of the database in mysql
+        :param create_schema: if True, create the schema on the database server
+        :param create_tables: if True, module.schema can be used as the decorator for declaring new
+        :param connection: a dj.Connection object to pass into the schema
+        :param add_objects: additional objects to add to the module
+        :return: the python module containing classes from the schema object and the table classes
+        """
+        super(VirtualModule, self).__init__(name=module_name)
+        _schema = Schema(schema_name, create_schema=create_schema, create_tables=create_tables,
+                            connection=connection)
+        if add_objects:
+            self.__dict__.update(add_objects)
+        self.__dict__['schema'] = _schema
+        _schema.spawn_missing_classes(context=self.__dict__)
 
 
 def list_schemas(connection=None):

datajoint/version.py

@@ -1,3 +1,3 @@
-__version__ = "0.12.4"
+__version__ = "0.12.5"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters

docs-parts/definition/01-Creating-Schemas_lang1.rst

@@ -2,21 +2,21 @@
 .. note:: By convention, the ``datajoint`` package is imported as ``dj``.
   The documentation refers to the package as ``dj`` throughout.
 
-Create a new schema using the ``dj.schema`` function:
+Create a new schema using the ``dj.Schema`` class object:
 
 .. code-block:: python
 
     import datajoint as dj
-    schema = dj.schema('alice_experiment')
+    schema = dj.Schema('alice_experiment')
 
 This statement creates the database schema ``alice_experiment`` on the server.
 
 The returned object ``schema`` will then serve as a decorator for DataJoint classes, as described in :ref:`table`.
 
 It is a common practice to have a separate Python module for each schema.
-Therefore, each such module has only one ``dj.schema`` object defined and is usually named ``schema``.
+Therefore, each such module has only one ``dj.Schema`` object defined and is usually named ``schema``.
 
-The ``dj.schema`` constructor can take a number of optional parameters after the schema name.
+The ``dj.Schema`` constructor can take a number of optional parameters after the schema name.
 
 - ``context`` - Dictionary for looking up foreign key references.
   Defaults to ``None`` to use local context.

docs-parts/definition/02-Creating-Tables_lang1.rst

@@ -12,7 +12,7 @@ For example, the following code defines the table ``Person``:
 .. code-block:: python
 
 	import datajoint as dj
-	schema = dj.schema('alice_experiment')
+	schema = dj.Schema('alice_experiment')
 
 	@schema
 	class Person(dj.Manual):

docs-parts/definition/11-ERD_lang1.rst

@@ -4,7 +4,7 @@ To plot the ERD for an entire schema, an ERD object can be initialized with the
 .. code-block:: python
 
     import datajoint as dj
-    schema = dj.schema('my_database')
+    schema = dj.Schema('my_database')
     dj.ERD(schema).draw()
 
 or alternatively an object that has the schema object as an attribute, such as the module defining a schema:

docs-parts/existing/0-Virtual-Modules_lang1.rst

@@ -1,4 +1,4 @@
-The function ``create_virtual_module`` of the ``dj.schema`` class provides access to virtual modules.
+The class object ``VirtualModule`` of the ``dj.Schema`` class provides access to virtual modules.
 It creates a python module with the given name from the name of a schema on the server, automatically adds classes to it corresponding to the tables in the schema.
 
 The function can take several parameters: