diff --git a/toardb/auth_user/models.py b/toardb/auth_user/models.py
index 5f644ed4c381c523e00a4352bd14c9e94dd2ece2..9284dd15d552b0e9932e39167e3d049a05da65d4 100644
--- a/toardb/auth_user/models.py
+++ b/toardb/auth_user/models.py
@@ -1,15 +1,17 @@
# coding: utf-8
-from sqlalchemy import ARRAY, BigInteger, Boolean, CheckConstraint, Column, DateTime, Float, ForeignKey, Index, Integer, SmallInteger, String, Table, Text, UniqueConstraint, text
+from sqlalchemy import ARRAY, BigInteger, Boolean, CheckConstraint, Column, DateTime, Float, ForeignKey, \
+ Index, Integer, SmallInteger, String, Table, Text, UniqueConstraint, text, Sequence
from sqlalchemy.orm import relationship
from geoalchemy2.types import Geometry
from sqlalchemy.dialects.postgresql import JSONB
from toardb.base import Base
+AUTH_USER_ID_SEQ = Sequence('auth_user_id_seq') # define sequence explicitly
class AuthUser(Base):
__tablename__ = 'auth_user'
- id = Column(Integer, primary_key=True, server_default=text("nextval('auth_user_id_seq'::regclass)"))
+ id = Column(Integer, AUTH_USER_ID_SEQ, primary_key=True, server_default=AUTH_USER_ID_SEQ.next_value())
password = Column(String(128), nullable=False)
last_login = Column(DateTime(True))
is_superuser = Column(Boolean, nullable=False)
diff --git a/toardb/contacts/contacts.py b/toardb/contacts/contacts.py
index 9f578a8f459c003fd55dfb088fe2b18973fa515c..171a54914889ad444b8c909e366ef0d6fa187f30 100644
--- a/toardb/contacts/contacts.py
+++ b/toardb/contacts/contacts.py
@@ -6,19 +6,10 @@ from typing import List
from fastapi import APIRouter, Depends, HTTPException, Body
from sqlalchemy.orm import Session
from . import crud, schemas
-from toardb.utils.database import ToarDbSession
+from toardb.utils.database import ToarDbSession, get_db
router = APIRouter()
-# Dependency
-def get_db():
- try:
- db = ToarDbSession()
- yield db
- finally:
- db.close()
-
-
# plain views to post and get contacts
#get all entries of table persons
diff --git a/toardb/contacts/models_organisation.py b/toardb/contacts/models_organisation.py
index dcf8f9c7502b77a28149d72880b91481e889f18d..3befad731e35acd1bd3334a6668211ca1795595b 100644
--- a/toardb/contacts/models_organisation.py
+++ b/toardb/contacts/models_organisation.py
@@ -3,10 +3,10 @@
class Organisation (Base)
=========================
"""
-from sqlalchemy import CheckConstraint, Column, Integer, String, text
+from sqlalchemy import CheckConstraint, Column, Integer, String, Sequence
from toardb.base import Base
-
+ORGANISATIONS_ID_SEQ = Sequence('organisations_id_seq') # define sequence explicitly
class Organisation(Base):
""" Table "public.organisations"
@@ -41,7 +41,7 @@ class Organisation(Base):
CheckConstraint('kind >= 0'),
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('organisations_id_seq'::regclass)"))
+ id = Column(Integer, ORGANISATIONS_ID_SEQ, primary_key=True, server_default=ORGANISATIONS_ID_SEQ.next_value())
name = Column(String(32), nullable=False)
longname = Column(String(128), nullable=False)
kind = Column(Integer, nullable=False)
diff --git a/toardb/contacts/models_person.py b/toardb/contacts/models_person.py
index aa31af4c9c1658cc968c552eb3352ee262c2ca7e..54ce047ee190fe3dc8526e47d354860af961a0bb 100644
--- a/toardb/contacts/models_person.py
+++ b/toardb/contacts/models_person.py
@@ -3,9 +3,10 @@
class Person (Base)
===================
"""
-from sqlalchemy import Boolean, Column, Integer, String, text
+from sqlalchemy import Boolean, Column, Integer, String, Sequence
from toardb.base import Base
+PERSONS_ID_SEQ = Sequence('persons_id_seq') # define sequence explicitly
class Person(Base):
""" Table "public.persons"
@@ -30,7 +31,7 @@ class Person(Base):
"""
__tablename__ = 'persons'
- id = Column(Integer, primary_key=True, server_default=text("nextval('persons_id_seq'::regclass)"))
+ id = Column(Integer, PERSONS_ID_SEQ, primary_key=True, server_default=PERSONS_ID_SEQ.next_value())
name = Column(String(64), nullable=False)
email = Column(String(128), nullable=False)
phone = Column(String(32), nullable=False)
diff --git a/toardb/contacts/test_base.py b/toardb/contacts/test_base.py
deleted file mode 100644
index 70113f71186ca3e4a4b90b1a25e40878fcb77e3f..0000000000000000000000000000000000000000
--- a/toardb/contacts/test_base.py
+++ /dev/null
@@ -1,78 +0,0 @@
-#taken from: https://github.com/tiangolo/fastapi/issues/831
-import pytest
-from starlette.testclient import TestClient
-from typing import Optional, AsyncIterable
-from sqlalchemy import create_engine
-from sqlalchemy.engine import Engine as Database
-from sqlalchemy.orm import Session
-from sqlalchemy_utils import database_exists, create_database, drop_database
-
-from toardb.utils.database import DATABASE_URL
-from .models import Base
-from toardb.toardb import app
-from toardb.contacts.contacts import get_db
-
-url = str(DATABASE_URL+ "_test")
-_db_conn = create_engine(url)
-
-def get_test_db_conn() -> Database:
- assert _db_conn is not None
- return _db_conn
-
-
-def get_test_db() -> AsyncIterable[Session]:
- sess = Session(bind=_db_conn)
-
- try:
- yield sess
- finally:
- sess.close()
-
-
-@pytest.fixture(scope="session", autouse=True)
-def create_test_database():
- """
- Create a clean database on every test case.
- We use the `sqlalchemy_utils` package here for a few helpers in consistently
- creating and dropping the database.
- """
- if database_exists(url):
- drop_database(url)
- create_database(url) # Create the test database.
- #'create_all' does not work (because of undefined id_seq table)!
- # I also need the id_seq tables:
- fake_conn = _db_conn.raw_connection()
- fake_cur = fake_conn.cursor()
- fake_cur.execute("CREATE SEQUENCE public.persons_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.organisations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- Base.metadata.create_all(_db_conn) # Create the tables.
- #try with the basics
- app.dependency_overrides[get_db] = get_test_db # Mock the Database Dependency
- yield # Run the tests.
- drop_database(url) # Drop the test database.
-
-
-@pytest.yield_fixture
-def test_db_session():
- """Returns an sqlalchemy session, and after the test tears down everything properly."""
-
- session = Session(bind=_db_conn)
-
- yield session
- # Drop all data after each test
- for tbl in reversed(Base.metadata.sorted_tables):
- _db_conn.execute(tbl.delete())
- # put back the connection to the connection pool
- session.close()
-
-
-@pytest.fixture()
-def client():
- """
- When using the 'client' fixture in test cases, we'll get full database
- rollbacks between test cases:
- """
- with TestClient(app) as client:
- yield client
diff --git a/toardb/contacts/test_contacts.py b/toardb/contacts/test_contacts.py
index 162883b20e596170a97f5857d66dd9c5e3c35290..06b3e9861b46c40a897560a461442804f265cea5 100644
--- a/toardb/contacts/test_contacts.py
+++ b/toardb/contacts/test_contacts.py
@@ -2,14 +2,14 @@ import pytest
import json
from .models import Person, Organisation
# Required imports 'create_test_database'
-from .test_base import (
+from toardb.test_base import (
client,
get_test_db,
create_test_database,
url,
+ get_test_engine,
test_db_session as db,
)
-from .test_base import _db_conn
class TestApps:
def setup(self):
@@ -23,6 +23,7 @@ class TestApps:
@pytest.fixture(autouse=True)
def setup_db_data(self, db):
# id_seq will not be reset automatically between tests!
+ _db_conn = get_test_engine()
fake_conn = _db_conn.raw_connection()
fake_cur = fake_conn.cursor()
fake_cur.execute("ALTER SEQUENCE persons_id_seq RESTART WITH 1")
diff --git a/toardb/data/data.py b/toardb/data/data.py
index c8a76b03b518dbb9cda1a2e80ef8a5048666034b..f61b31f7eb225dbf675ee437f347146a1c5fbb29 100644
--- a/toardb/data/data.py
+++ b/toardb/data/data.py
@@ -9,24 +9,10 @@ from fastapi import APIRouter, Depends, HTTPException, \
from sqlalchemy.orm import Session
from sqlalchemy.engine import Engine
from . import crud, schemas
-from toardb.utils.database import ToarDbSession, engine
+from toardb.utils.database import ToarDbSession, engine, get_engine, get_db
router = APIRouter()
-# Dependency
-def get_engine():
- assert engine is not None
- return engine
-
-# Dependency
-def get_db():
- try:
- db = ToarDbSession()
- yield db
- finally:
- db.close()
-
-
# plain views to post and get data
#get all data of table data
diff --git a/toardb/data/test_base.py b/toardb/data/test_base.py
deleted file mode 100644
index d85318992098d439453904db993fdffe77981668..0000000000000000000000000000000000000000
--- a/toardb/data/test_base.py
+++ /dev/null
@@ -1,124 +0,0 @@
-#taken from: https://github.com/tiangolo/fastapi/issues/831
-import pytest
-from starlette.testclient import TestClient
-from typing import Optional, AsyncIterable
-from sqlalchemy import create_engine
-from sqlalchemy.engine import Engine
-from sqlalchemy.orm import Session
-from sqlalchemy.orm import sessionmaker
-from sqlalchemy_utils import database_exists, create_database, drop_database
-
-from toardb.utils.database import DATABASE_URL
-from .models import Base
-from toardb.auth_user.models import Base as AuthUserBase
-from toardb.contacts.models import Base as ContactBase
-from toardb.variables.models import Base as VariableBase
-from toardb.stationmeta.models import Base as StationmetaBase
-from toardb.timeseries.models import Base as TimeseriesBase
-from toardb.toardb import app
-from toardb.data.data import get_db, get_engine
-
-url = str(DATABASE_URL+ "_test")
-_db_conn = create_engine(url)
-
-def get_test_engine() -> Engine:
- assert _db_conn is not None
- return _db_conn
-
-
-def get_test_db():
- sess = sessionmaker(bind=_db_conn,autoflush=False,autocommit=False)()
- try:
- yield sess
- finally:
- sess.close()
-
-
-@pytest.fixture(scope="session", autouse=True)
-def create_test_database():
- """
- Create a clean database on every test case.
- We use the `sqlalchemy_utils` package here for a few helpers in consistently
- creating and dropping the database.
- """
- if database_exists(url):
- drop_database(url)
- create_database(url) # Create the test database.
- #'create_all' does not work (because of undefined 'Geometry')!
- #declare PostGIS extension!
- fake_conn = _db_conn.raw_connection()
- fake_cur = fake_conn.cursor()
- fake_cur.execute("CREATE EXTENSION postgis")
- fake_conn.commit()
- # I also need the id_seq tables:
- fake_cur.execute("CREATE SEQUENCE public.auth_user_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.variables_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_core_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_global_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_global_services_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_roles_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_annotations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_docs_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_images_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_urls_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.persons_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.organisations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_annotations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_roles_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_programmes_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- AuthUserBase.metadata.create_all(_db_conn) # Create the tables.
- ContactBase.metadata.create_all(_db_conn) # Create the tables.
- VariableBase.metadata.create_all(_db_conn) # Create the tables.
- StationmetaBase.metadata.create_all(_db_conn) # Create the tables.
- TimeseriesBase.metadata.create_all(_db_conn) # Create the tables.
- Base.metadata.create_all(_db_conn) # Create the tables.
- #try with the basics
- app.dependency_overrides[get_db] = get_test_db # Mock the Database Dependency
- app.dependency_overrides[get_engine] = get_test_engine # Mock the Database Dependency
- yield # Run the tests.
- drop_database(url) # Drop the test database.
-
-
-@pytest.yield_fixture
-def test_db_session():
- """Returns an sqlalchemy session, and after the test tears down everything properly."""
-
- session = sessionmaker(bind=_db_conn,autoflush=False,autocommit=False)()
- yield session
- # Drop all data after each test
- for tbl in reversed(AuthUserBase.metadata.sorted_tables +
- ContactBase.metadata.sorted_tables +
- VariableBase.metadata.sorted_tables +
- StationmetaBase.metadata.sorted_tables +
- TimeseriesBase.metadata.sorted_tables +
- Base.metadata.sorted_tables):
- _db_conn.execute(tbl.delete())
- # put back the connection to the connection pool
- session.close()
-
-
-@pytest.fixture()
-def client():
- """
- When using the 'client' fixture in test cases, we'll get full database
- rollbacks between test cases:
- """
- with TestClient(app) as client:
- yield client
diff --git a/toardb/data/test_data.py b/toardb/data/test_data.py
index 30915342376035c6f070ef03cd470be53f17f332..b3354a77addaaf362c75b67448386330c440c94d 100644
--- a/toardb/data/test_data.py
+++ b/toardb/data/test_data.py
@@ -7,15 +7,14 @@ from toardb.stationmeta.schemas import get_geom_from_coordinates, Coordinates
from toardb.variables.models import Variable
from toardb.contacts.models import Person, Organisation
from toardb.auth_user.models import AuthUser
-# Required imports 'create_test_database'
-from .test_base import (
+from toardb.test_base import (
client,
get_test_db,
create_test_database,
url,
+ get_test_engine,
test_db_session as db,
)
-from .test_base import _db_conn
class TestApps:
def setup(self):
@@ -28,6 +27,7 @@ class TestApps:
"""
@pytest.fixture(autouse=True)
def setup_db_data(self, db):
+ _db_conn = get_test_engine()
fake_conn = _db_conn.raw_connection()
fake_cur = fake_conn.cursor()
# id_seq will not be reset automatically between tests!
@@ -45,11 +45,11 @@ class TestApps:
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE stationmeta_annotations_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_docs_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_doc_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_images_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_image_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_urls_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_url_id_seq RESTART WITH 1")
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE persons_id_seq RESTART WITH 1")
fake_conn.commit()
diff --git a/toardb/stationmeta/models_annotation.py b/toardb/stationmeta/models_annotation.py
index fd31faf860b1d78bc16fb4bc327d1d440b88764b..c7f91b67ab8e9a1a6fccbe0ce962e801c6e1e4f7 100644
--- a/toardb/stationmeta/models_annotation.py
+++ b/toardb/stationmeta/models_annotation.py
@@ -3,8 +3,8 @@
class StationmetaAnnotation (Base)
==================================
"""
-from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, String, \
- Text, Boolean, CheckConstraint, Table
+from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, String, \
+ Text, Boolean, CheckConstraint, Table, Sequence
from sqlalchemy.orm import relationship
from toardb.auth_user.models import AuthUser
from toardb.base import Base
@@ -17,24 +17,25 @@ stationmeta_core_stationmeta_annotations_table = Table('stationmeta_core_station
)
+STATIONMETA_ANNOTATIONS_ID_SEQ = Sequence('stationmeta_annotations_id_seq') # define sequence explicitly
class StationmetaAnnotation(Base):
""" Table "public.stationmeta_annotations"
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
- | Column | Type | Collation | Nullable | Default |
- +================+==========================+===========+==========+====================================================+
- | id | integer | | not null | nextval('station_annotations_id_seq'::regclass) |
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
- | kind | integer | | not null | |
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
- | text | text | | not null | |
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
- | date_added | timestamp with time zone | | not null | |
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
- | approved | boolean | | not null | |
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
- | contributor_id | integer | | not null | |
- +----------------+--------------------------+-----------+----------+----------------------------------------------------+
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
+ | Column | Type | Collation | Nullable | Default |
+ +================+==========================+===========+==========+========================================================+
+ | id | integer | | not null | nextval('stationmeta_annotations_id_seq'::regclass) |
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
+ | kind | integer | | not null | |
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
+ | text | text | | not null | |
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
+ | date_added | timestamp with time zone | | not null | |
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
+ | approved | boolean | | not null | |
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
+ | contributor_id | integer | | not null | |
+ +----------------+--------------------------+-----------+----------+--------------------------------------------------------+
Indexes:
"stationmeta_annotations_pkey" PRIMARY KEY, btree (id)
"stationmeta_annotations_contributor_id_a5009820" btree (contributor_id)
@@ -48,7 +49,7 @@ class StationmetaAnnotation(Base):
CheckConstraint('kind >= 0'),
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_annotations_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_ANNOTATIONS_ID_SEQ, primary_key=True, server_default=STATIONMETA_ANNOTATIONS_ID_SEQ.next_value())
kind = Column(Integer, nullable=False)
text = Column(Text, nullable=False)
date_added = Column(DateTime(True), nullable=False)
diff --git a/toardb/stationmeta/models_aux.py b/toardb/stationmeta/models_aux.py
index 3f754c7e413bcb83515b07c6da4af46540a349c6..eb42b8675e94fe0bb2b242641ec2f4b2c27b7556 100644
--- a/toardb/stationmeta/models_aux.py
+++ b/toardb/stationmeta/models_aux.py
@@ -12,12 +12,13 @@ class StationMetaAuxDoc (Base)
class StationMetaAuxImage (Base)
--------------------------------
"""
-from sqlalchemy import CheckConstraint, Column, DateTime, ForeignKey, Integer, String, Text, text
+from sqlalchemy import CheckConstraint, Column, DateTime, ForeignKey, Integer, String, Text, Sequence
#from sqlalchemy.orm import relationship
from .models_core import StationmetaCore
from toardb.base import Base
+STATIONMETA_AUX_DOC_ID_SEQ = Sequence('stationmeta_aux_doc_id_seq') #define sequence explicitly
class StationmetaAuxDoc(Base):
""" Table "public.stationmeta_aux_doc"
@@ -43,7 +44,7 @@ class StationmetaAuxDoc(Base):
__tablename__ = 'stationmeta_aux_doc'
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_aux_docs_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_AUX_DOC_ID_SEQ, primary_key=True, server_default=STATIONMETA_AUX_DOC_ID_SEQ.next_value())
resource_description = Column(Text, nullable=False)
date_added = Column(DateTime(True), nullable=False)
resource = Column(String(100), nullable=False)
@@ -52,6 +53,7 @@ class StationmetaAuxDoc(Base):
# station = relationship('StationmetaCore')
+STATIONMETA_AUX_IMAGE_ID_SEQ = Sequence('stationmeta_aux_image_id_seq') #define sequence explicitly
class StationmetaAuxImage(Base):
""" Table "public.stationmeta_aux_image"
@@ -88,7 +90,7 @@ class StationmetaAuxImage(Base):
CheckConstraint('image_width >= 0')
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_aux_images_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_AUX_IMAGE_ID_SEQ, primary_key=True, server_default=STATIONMETA_AUX_IMAGE_ID_SEQ.next_value())
resource_description = Column(Text, nullable=False)
date_added = Column(DateTime(True), nullable=False)
resource = Column(String(100), nullable=False)
@@ -99,6 +101,7 @@ class StationmetaAuxImage(Base):
# station = relationship('StationmetaCore')
+STATIONMETA_AUX_URL_ID_SEQ = Sequence('stationmeta_aux_url_id_seq') #define sequence explicitly
class StationmetaAuxUrl(Base):
""" Table "public.stationmeta_aux_url"
@@ -124,7 +127,7 @@ class StationmetaAuxUrl(Base):
__tablename__ = 'stationmeta_aux_url'
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_aux_urls_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_AUX_URL_ID_SEQ, primary_key=True, server_default=STATIONMETA_AUX_URL_ID_SEQ.next_value())
resource_description = Column(Text, nullable=False)
date_added = Column(DateTime(True), nullable=False)
resource = Column(String(200), nullable=False)
diff --git a/toardb/stationmeta/models_core.py b/toardb/stationmeta/models_core.py
index e4498c74d968ccd7035cdea8b7427b02b0cb25d3..7b4d23c67cf541e17157297416a633da16da236a 100644
--- a/toardb/stationmeta/models_core.py
+++ b/toardb/stationmeta/models_core.py
@@ -3,8 +3,8 @@
class StationmetaCore (Base)
============================
"""
-from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, String, \
- Text, CheckConstraint
+from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, String, \
+ Text, CheckConstraint, Sequence
from geoalchemy2.types import Geometry
from sqlalchemy.orm import relationship
from sqlalchemy.dialects.postgresql import JSONB, ARRAY
@@ -12,7 +12,7 @@ from shapely import wkt
from toardb.auth_user.models import AuthUser
from toardb.base import Base
-
+STATIONMETA_CORE_ID_SEQ = Sequence('stationmeta_core_id_seq') # define sequence explicitly
class StationmetaCore(Base):
""" Table "public.stationmeta_core"
@@ -78,7 +78,7 @@ class StationmetaCore(Base):
CheckConstraint('type_of_environment >= 0')
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_core_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_CORE_ID_SEQ, primary_key=True, server_default=STATIONMETA_CORE_ID_SEQ.next_value())
codes = Column(ARRAY(String(16)))
name = Column(String(128), nullable=False)
coordinates = Column(Geometry('POINTZ', 4326))
diff --git a/toardb/stationmeta/models_global.py b/toardb/stationmeta/models_global.py
index a4960507b6eb70f0cab0700edbb2ecd9d9d017ba..f9cea75e62769dcba3eb36516631d36edda66b6a 100644
--- a/toardb/stationmeta/models_global.py
+++ b/toardb/stationmeta/models_global.py
@@ -3,15 +3,15 @@
class StationmetaGlobal (Base)
==============================
"""
-from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, String, \
- Text, CheckConstraint
+from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, String, \
+ Text, CheckConstraint, Sequence
from geoalchemy2.types import Geometry
from sqlalchemy.orm import relationship
from sqlalchemy.dialects.postgresql import JSONB, ARRAY
from .models_core import StationmetaCore
from toardb.base import Base
-
+STATIONMETA_GLOBAL_ID_SEQ = Sequence('stationmeta_global_id_seq') # define sequence explicitly
class StationmetaGlobal(Base):
""" Table "public.stationmeta_global"
@@ -73,7 +73,7 @@ class StationmetaGlobal(Base):
CheckConstraint('toar1_category >= 0')
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_global_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_GLOBAL_ID_SEQ, primary_key=True, server_default=STATIONMETA_GLOBAL_ID_SEQ.next_value())
population_density_year2010 = Column(Float(53), nullable=False)
max_population_density_25km_year2010 = Column(Float(53), nullable=False)
climatic_zone = Column(Integer, nullable=False)
diff --git a/toardb/stationmeta/models_global_services.py b/toardb/stationmeta/models_global_services.py
index a0c99b7c661c4c3ec5a82d9e9a578da684e1ffc1..5f8f7daf0f9688e52c3aaefe25c3caa387965a2c 100644
--- a/toardb/stationmeta/models_global_services.py
+++ b/toardb/stationmeta/models_global_services.py
@@ -3,9 +3,10 @@
class StationmetaGlobalService (Base)
=====================================
"""
-from sqlalchemy import CheckConstraint, Column, Integer, String, text
+from sqlalchemy import CheckConstraint, Column, Integer, String, Sequence
from toardb.base import Base
+STATIONMETA_GLOBAL_SERVICES_ID_SEQ = Sequence('stationmeta_global_services_id_seq') # define sequence explicitly
class StationmetaGlobalService(Base):
""" Table "public.stationmeta_global_services"
@@ -41,7 +42,7 @@ class StationmetaGlobalService(Base):
CheckConstraint('service_valid_year >= 0')
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_global_services_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_GLOBAL_SERVICES_ID_SEQ, primary_key=True, server_default=STATIONMETA_GLOBAL_SERVICES_ID_SEQ.next_value())
variable_name = Column(String(64), nullable=False)
result_type = Column(Integer, nullable=False)
result_nvalues = Column(Integer, nullable=False)
diff --git a/toardb/stationmeta/models_role.py b/toardb/stationmeta/models_role.py
index 4d6b6602ef54d7324ee6c4a4fb166b4426eabe11..01fd6d3d751fa4ade7c9daba983d0c35938ec819 100644
--- a/toardb/stationmeta/models_role.py
+++ b/toardb/stationmeta/models_role.py
@@ -3,8 +3,8 @@
class StationmetaRole (Base)
============================
"""
-from sqlalchemy import Column, ForeignKey, Integer, text, \
- CheckConstraint, UniqueConstraint, Table
+from sqlalchemy import Column, ForeignKey, Integer, \
+ CheckConstraint, UniqueConstraint, Table, Sequence
from sqlalchemy.orm import relationship
from toardb.contacts.models import Person
from toardb.base import Base
@@ -17,20 +17,21 @@ stationmeta_core_stationmeta_roles_table = Table('stationmeta_core_timeseries_ro
)
+STATIONMETA_ROLES_ID_SEQ = Sequence('stationmeta_roles_id_seq') # define sequence explicitly
class StationmetaRole(Base):
""" Table "public.stationmeta_roles"
- +------------+---------+-----------+----------+-------------------------------------------+
- | Column | Type | Collation | Nullable | Default |
- +============+=========+===========+==========+===========================================+
- | id | integer | | not null | nextval('station_roles_id_seq'::regclass) |
- +------------+---------+-----------+----------+-------------------------------------------+
- | role | integer | | not null | |
- +------------+---------+-----------+----------+-------------------------------------------+
- | status | integer | | not null | |
- +------------+---------+-----------+----------+-------------------------------------------+
- | person_id | integer | | not null | |
- +------------+---------+-----------+----------+-------------------------------------------+
+ +------------+---------+-----------+----------+-----------------------------------------------+
+ | Column | Type | Collation | Nullable | Default |
+ +============+=========+===========+==========+===============================================+
+ | id | integer | | not null | nextval('stationmeta_roles_id_seq'::regclass) |
+ +------------+---------+-----------+----------+-----------------------------------------------+
+ | role | integer | | not null | |
+ +------------+---------+-----------+----------+-----------------------------------------------+
+ | status | integer | | not null | |
+ +------------+---------+-----------+----------+-----------------------------------------------+
+ | person_id | integer | | not null | |
+ +------------+---------+-----------+----------+-----------------------------------------------+
Indexes:
"stationmeta_roles_pkey" PRIMARY KEY, btree (id)
"stationmeta_roles_person_id_3bd9c160" btree (person_id)
@@ -47,7 +48,7 @@ class StationmetaRole(Base):
CheckConstraint('status >= 0')
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('stationmeta_roles_id_seq'::regclass)"))
+ id = Column(Integer, STATIONMETA_ROLES_ID_SEQ, primary_key=True, server_default=STATIONMETA_ROLES_ID_SEQ.next_value())
role = Column(Integer, nullable=False)
status = Column(Integer, nullable=False)
# do not use string declaration here (not working for pytest)
diff --git a/toardb/stationmeta/stationmeta.py b/toardb/stationmeta/stationmeta.py
index 6367f09d1902bb18937c54b353cff30fcb68a32a..a3c100336d13ee89d2df9fa6e598e321178ca0a4 100644
--- a/toardb/stationmeta/stationmeta.py
+++ b/toardb/stationmeta/stationmeta.py
@@ -7,34 +7,10 @@ from fastapi import APIRouter, Depends, HTTPException, Body
from sqlalchemy.orm import Session, sessionmaker
from . import crud, schemas
from sqlalchemy import create_engine
-from toardb.utils.database import DATABASE_URL
+from toardb.utils.database import DATABASE_URL, get_db
router = APIRouter()
-# Dependency
-#def get_db():
-# try:
-# db = ToarDbSession()
-# yield db
-# finally:
-# db.close()
-
-# the following to be able to test!
-# will later go to utils.database again!
-# Dependency
-async def get_db():
- engine = create_engine(
- DATABASE_URL, #connect_args={"check_same_thread": False}
- )
- SessionLocal = sessionmaker(bind=engine)
-
- try:
- db = SessionLocal()
- yield db
- finally:
- db.close()
-
-
# plain views to post and get stationmeta
#get all entries of table stationmeta
diff --git a/toardb/stationmeta/test_base.py b/toardb/stationmeta/test_base.py
deleted file mode 100644
index 55575696b5b2021a36e1776537329e6dfb80ad59..0000000000000000000000000000000000000000
--- a/toardb/stationmeta/test_base.py
+++ /dev/null
@@ -1,99 +0,0 @@
-#taken from: https://github.com/tiangolo/fastapi/issues/831
-import pytest
-from starlette.testclient import TestClient
-from typing import Optional, AsyncIterable
-from sqlalchemy import create_engine
-from sqlalchemy.engine import Engine as Database
-from sqlalchemy.orm import Session
-from sqlalchemy_utils import database_exists, create_database, drop_database
-
-from toardb.utils.database import DATABASE_URL
-from .models import Base
-from toardb.toardb import app
-from toardb.stationmeta.stationmeta import get_db
-
-url = str(DATABASE_URL+ "_test")
-_db_conn = create_engine(url)
-
-def get_test_db_conn() -> Database:
- assert _db_conn is not None
- return _db_conn
-
-
-def get_test_db() -> AsyncIterable[Session]:
- sess = Session(bind=_db_conn)
-
- try:
- yield sess
- finally:
- sess.close()
-
-
-@pytest.fixture(scope="session", autouse=True)
-def create_test_database():
- """
- Create a clean database on every test case.
- We use the `sqlalchemy_utils` package here for a few helpers in consistently
- creating and dropping the database.
- """
- if database_exists(url):
- drop_database(url)
- create_database(url) # Create the test database.
- #'create_all' does not work (because of undefined 'Geometry')!
- #declare PostGIS extension!
- fake_conn = _db_conn.raw_connection()
- fake_cur = fake_conn.cursor()
- fake_cur.execute("CREATE EXTENSION postgis")
- fake_conn.commit()
- # I also need the id_seq tables:
- fake_cur.execute("CREATE SEQUENCE public.auth_user_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_core_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_global_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_global_services_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_annotations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_roles_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_docs_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_images_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_urls_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.persons_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.organisations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- Base.metadata.create_all(_db_conn) # Create the tables.
- #try with the basics
- app.dependency_overrides[get_db] = get_test_db # Mock the Database Dependency
- yield # Run the tests.
- drop_database(url) # Drop the test database.
-
-
-@pytest.yield_fixture
-def test_db_session():
- """Returns an sqlalchemy session, and after the test tears down everything properly."""
-
- session = Session(bind=_db_conn)
-
- yield session
- # Drop all data after each test
- for tbl in reversed(Base.metadata.sorted_tables):
- _db_conn.execute(tbl.delete())
- # put back the connection to the connection pool
- session.close()
-
-
-@pytest.fixture()
-def client():
- """
- When using the 'client' fixture in test cases, we'll get full database
- rollbacks between test cases:
- """
- with TestClient(app) as client:
- yield client
diff --git a/toardb/stationmeta/test_stationmeta.py b/toardb/stationmeta/test_stationmeta.py
index b7b9a184fcc1af1801ca5417c014b57bacece194..792815418c373aa28b78b409b693dc144c700b98 100644
--- a/toardb/stationmeta/test_stationmeta.py
+++ b/toardb/stationmeta/test_stationmeta.py
@@ -4,15 +4,14 @@ from .models import StationmetaCore
from toardb.auth_user.models import AuthUser
from toardb.contacts.models import Person, Organisation
from .schemas import get_geom_from_coordinates, Coordinates
-# Required imports 'create_test_database'
-from .test_base import (
+from toardb.test_base import (
client,
get_test_db,
create_test_database,
url,
+ get_test_engine,
test_db_session as db,
)
-from .test_base import _db_conn
class TestApps:
def setup(self):
@@ -26,6 +25,7 @@ class TestApps:
@pytest.fixture(autouse=True)
def setup_db_data(self, db):
# id_seq will not be reset automatically between tests!
+ _db_conn = get_test_engine()
fake_conn = _db_conn.raw_connection()
fake_cur = fake_conn.cursor()
fake_cur.execute("ALTER SEQUENCE auth_user_id_seq RESTART WITH 1")
@@ -40,11 +40,11 @@ class TestApps:
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE stationmeta_roles_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_docs_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_doc_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_images_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_image_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_urls_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_url_id_seq RESTART WITH 1")
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE persons_id_seq RESTART WITH 1")
fake_conn.commit()
diff --git a/toardb/variables/test_base.py b/toardb/test_base.py
similarity index 73%
rename from toardb/variables/test_base.py
rename to toardb/test_base.py
index a8b05f14a0129f3f2f12a3802f091833c16b9063..ff85b1aae866c86493552fd7b6897a91c126c2e7 100644
--- a/toardb/variables/test_base.py
+++ b/toardb/test_base.py
@@ -1,28 +1,25 @@
#taken from: https://github.com/tiangolo/fastapi/issues/831
import pytest
from starlette.testclient import TestClient
-from typing import Optional, AsyncIterable
from sqlalchemy import create_engine
-from sqlalchemy.engine import Engine as Database
-from sqlalchemy.orm import Session
+from sqlalchemy.engine import Engine
+from sqlalchemy.orm import sessionmaker
from sqlalchemy_utils import database_exists, create_database, drop_database
-from toardb.utils.database import DATABASE_URL
-from .models import Base
+from toardb.base import Base
from toardb.toardb import app
-from toardb.variables.variables import get_db
+from toardb.utils.database import DATABASE_URL, get_db, get_engine
url = str(DATABASE_URL+ "_test")
_db_conn = create_engine(url)
-def get_test_db_conn() -> Database:
+def get_test_engine() -> Engine:
assert _db_conn is not None
return _db_conn
-def get_test_db() -> AsyncIterable[Session]:
- sess = Session(bind=_db_conn)
-
+def get_test_db():
+ sess = sessionmaker(bind=_db_conn,autoflush=False,autocommit=False)()
try:
yield sess
finally:
@@ -40,17 +37,17 @@ def create_test_database():
drop_database(url)
create_database(url) # Create the test database.
#'create_all' does not work (because of undefined 'Geometry')!
- #declare PostGIS extension!
+ #declare PostGIS extension! (and toar_controlled_vocabulary)
fake_conn = _db_conn.raw_connection()
fake_cur = fake_conn.cursor()
- fake_cur.execute("CREATE EXTENSION postgis")
+ fake_cur.execute("CREATE EXTENSION IF NOT EXISTS postgis")
fake_conn.commit()
- # I also need the id_seq tables:
- fake_cur.execute("CREATE SEQUENCE public.variables_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
+ fake_cur.execute("CREATE EXTENSION IF NOT EXISTS toar_controlled_vocabulary")
fake_conn.commit()
Base.metadata.create_all(_db_conn) # Create the tables.
#try with the basics
app.dependency_overrides[get_db] = get_test_db # Mock the Database Dependency
+ app.dependency_overrides[get_engine] = get_test_engine # Mock the Database Dependency
yield # Run the tests.
drop_database(url) # Drop the test database.
@@ -59,8 +56,7 @@ def create_test_database():
def test_db_session():
"""Returns an sqlalchemy session, and after the test tears down everything properly."""
- session = Session(bind=_db_conn)
-
+ session = sessionmaker(bind=_db_conn,autoflush=False,autocommit=False)()
yield session
# Drop all data after each test
for tbl in reversed(Base.metadata.sorted_tables):
diff --git a/toardb/timeseries/models_annotation.py b/toardb/timeseries/models_annotation.py
index 43b0c3ef5c72985afa130af42e378fded4276383..e24a9624a8e0209b50349c26e610fd07bfe047c3 100644
--- a/toardb/timeseries/models_annotation.py
+++ b/toardb/timeseries/models_annotation.py
@@ -4,7 +4,7 @@ class TimeseriesAnnotation(Base)
================================
"""
from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, String, \
- Text, Boolean, CheckConstraint, Table
+ Text, Boolean, CheckConstraint, Table, Sequence
from sqlalchemy.orm import relationship
from toardb.auth_user.models import AuthUser
from toardb.base import Base
@@ -16,6 +16,7 @@ timeseries_timeseries_annotations_table = Table('timeseries_timeseries_annotatio
)
+TIMESERIES_ANNOTATIONS_ID_SEQ = Sequence('timeseries_annotations_id_seq') # define sequence explicitly
class TimeseriesAnnotation(Base):
""" Table "public.timeseries_annotations"
@@ -47,7 +48,7 @@ class TimeseriesAnnotation(Base):
CheckConstraint('kind >= 0'),
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('timeseries_annotations_id_seq'::regclass)"))
+ id = Column(Integer, TIMESERIES_ANNOTATIONS_ID_SEQ, primary_key=True, server_default=TIMESERIES_ANNOTATIONS_ID_SEQ.next_value())
kind = Column(Integer, nullable=False)
text = Column(Text, nullable=False)
date_added = Column(DateTime(True), nullable=False)
diff --git a/toardb/timeseries/models_core.py b/toardb/timeseries/models_core.py
index 81df7e15fe71d574410cfae85ad235550dd6b35a..b69d0e0627b573e347a84d582ba8d6a7a7e9e22b 100644
--- a/toardb/timeseries/models_core.py
+++ b/toardb/timeseries/models_core.py
@@ -4,13 +4,15 @@ class Timeseries (Base)
=======================
"""
from sqlalchemy import Column, DateTime, Float, ForeignKey, Integer, text, String, \
- Text, CheckConstraint, UniqueConstraint, PrimaryKeyConstraint
+ Text, CheckConstraint, UniqueConstraint, PrimaryKeyConstraint, \
+ Sequence
from sqlalchemy.dialects.postgresql import JSONB
from toardb.stationmeta.models import StationmetaCore
from toardb.variables.models import Variable
from toardb.base import Base
+TIMESERIES_ID_SEQ = Sequence('timeseries_id_seq') # define sequence explicitly
class Timeseries(Base):
""" Table "public.timeseries"
@@ -76,7 +78,7 @@ class Timeseries(Base):
UniqueConstraint('station_id', 'variable_id', 'label'),
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('timeseries_id_seq'::regclass)"))
+ id = Column(Integer, TIMESERIES_ID_SEQ, primary_key=True, server_default=TIMESERIES_ID_SEQ.next_value())
label = Column(String(128), nullable=False)
order = Column(Integer, nullable=False)
access_rights = Column(Integer, nullable=False)
diff --git a/toardb/timeseries/models_programme.py b/toardb/timeseries/models_programme.py
index d293905a436ba0a54d97c900137c24cd359672c1..fc44d596527dbecfb18b7deda4d4de62aa1544ee 100644
--- a/toardb/timeseries/models_programme.py
+++ b/toardb/timeseries/models_programme.py
@@ -3,7 +3,7 @@
class TimeseriesProgramme (Base)
================================
"""
-from sqlalchemy import Column, Integer, text, String, Text, ForeignKey, Table
+from sqlalchemy import Column, Integer, text, String, Text, ForeignKey, Table, Sequence
from sqlalchemy.orm import relationship
from toardb.base import Base
@@ -13,7 +13,8 @@ timeseries_timeseries_programmes_table = Table('timeseries_timeseries_programmes
Column('programme_id', Integer, ForeignKey('timeseries_programmes.id'))
)
-# this has at the moment no relation to anything!!!
+
+TIMESERIES_PROGRAMMES_ID_SEQ = Sequence('timeseries_programmes_id_seq') # define sequence explicitly
class TimeseriesProgramme(Base):
""" Table "public.timeseries_programmes"
@@ -35,7 +36,7 @@ class TimeseriesProgramme(Base):
"""
__tablename__ = 'timeseries_programmes'
- id = Column(Integer, primary_key=True, server_default=text("nextval('timeseries_programmes_id_seq'::regclass)"))
+ id = Column(Integer, TIMESERIES_PROGRAMMES_ID_SEQ, primary_key=True, server_default=TIMESERIES_PROGRAMMES_ID_SEQ.next_value())
name = Column(String(32), nullable=False)
longname = Column(String(128), nullable=False)
homepage = Column(String(200), nullable=False)
diff --git a/toardb/timeseries/models_role.py b/toardb/timeseries/models_role.py
index fbfa87981337cba805b1d0ab18f85d4b786ca6c5..eca3f3e376a0ba16b1f9cce159e1e1cece422daa 100644
--- a/toardb/timeseries/models_role.py
+++ b/toardb/timeseries/models_role.py
@@ -5,7 +5,7 @@ class TimeseriesRole (Base)
"""
from sqlalchemy import Column, ForeignKey, Integer, text, \
CheckConstraint, UniqueConstraint, \
- Table
+ Table, Sequence
from sqlalchemy.orm import relationship
from toardb.contacts.models import Person
from toardb.base import Base
@@ -17,7 +17,7 @@ timeseries_timeseries_roles_table = Table('timeseries_timeseries_roles', Base.me
Column('role_id', Integer, ForeignKey('timeseries_roles.id'))
)
-
+TIMESERIES_ROLES_ID_SEQ = Sequence('timeseries_roles_id_seq') # define sequence explicitly
class TimeseriesRole(Base):
""" Table "public.timeseries_roles"
@@ -50,7 +50,7 @@ class TimeseriesRole(Base):
UniqueConstraint('role', 'person_id')
)
- id = Column(Integer, primary_key=True, server_default=text("nextval('timeseries_roles_id_seq'::regclass)"))
+ id = Column(Integer, TIMESERIES_ROLES_ID_SEQ, primary_key=True, server_default=TIMESERIES_ROLES_ID_SEQ.next_value())
role = Column(Integer, nullable=False)
status = Column(Integer, nullable=False)
# do not use string declaration here (not working for pytest)
diff --git a/toardb/timeseries/test_base.py b/toardb/timeseries/test_base.py
deleted file mode 100644
index 0906f4b5e617430be4ec3d332ba897506af947cd..0000000000000000000000000000000000000000
--- a/toardb/timeseries/test_base.py
+++ /dev/null
@@ -1,114 +0,0 @@
-#taken from: https://github.com/tiangolo/fastapi/issues/831
-import pytest
-from starlette.testclient import TestClient
-from typing import Optional, AsyncIterable
-from sqlalchemy import create_engine
-from sqlalchemy.engine import Engine as Database
-from sqlalchemy.orm import Session
-from sqlalchemy_utils import database_exists, create_database, drop_database
-
-from toardb.utils.database import DATABASE_URL
-from .models import Base
-from toardb.toardb import app
-from toardb.timeseries.timeseries import get_db
-
-url = str(DATABASE_URL+ "_test")
-_db_conn = create_engine(url)
-
-def get_test_db_conn() -> Database:
- assert _db_conn is not None
- return _db_conn
-
-
-def get_test_db() -> AsyncIterable[Session]:
- sess = Session(bind=_db_conn)
-
- try:
- yield sess
- finally:
- sess.close()
-
-
-@pytest.fixture(scope="session", autouse=True)
-def create_test_database():
- """
- Create a clean database on every test case.
- We use the `sqlalchemy_utils` package here for a few helpers in consistently
- creating and dropping the database.
- """
- if database_exists(url):
- drop_database(url)
- create_database(url) # Create the test database.
- #'create_all' does not work (because of undefined 'Geometry')!
- #declare PostGIS extension!
- fake_conn = _db_conn.raw_connection()
- fake_cur = fake_conn.cursor()
- fake_cur.execute("CREATE EXTENSION postgis")
- fake_conn.commit()
- # I also need the id_seq tables:
- fake_cur.execute("CREATE SEQUENCE public.auth_user_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.variables_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_core_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_global_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_global_services_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_roles_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_annotations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_docs_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_images_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.stationmeta_aux_urls_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.persons_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.organisations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_annotations_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_roles_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_programmes_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- fake_cur.execute("CREATE SEQUENCE public.timeseries_id_seq AS integer START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1")
- fake_conn.commit()
- # just to show that tables are available now:
-# fake_cur.execute("SELECT * FROM pg_catalog.pg_tables WHERE schemaname != 'pg_catalog' AND schemaname != 'information_schema'")
-# rows = fake_cur.fetchall()
-# for row in rows:
-# print(row)
- Base.metadata.create_all(_db_conn) # Create the tables.
- #try with the basics
- app.dependency_overrides[get_db] = get_test_db # Mock the Database Dependency
- yield # Run the tests.
- drop_database(url) # Drop the test database.
-
-
-@pytest.yield_fixture
-def test_db_session():
- """Returns an sqlalchemy session, and after the test tears down everything properly."""
-
- session = Session(bind=_db_conn)
-
- yield session
- # Drop all data after each test
- for tbl in reversed(Base.metadata.sorted_tables):
- _db_conn.execute(tbl.delete())
- # put back the connection to the connection pool
- session.close()
-
-
-@pytest.fixture()
-def client():
- """
- When using the 'client' fixture in test cases, we'll get full database
- rollbacks between test cases:
- """
- with TestClient(app) as client:
- yield client
diff --git a/toardb/timeseries/test_timeseries.py b/toardb/timeseries/test_timeseries.py
index 37f74fe46203162bdff0120099593e36c9802ebf..de006943d659ee6f24a99b2a667f0d5809908889 100644
--- a/toardb/timeseries/test_timeseries.py
+++ b/toardb/timeseries/test_timeseries.py
@@ -7,14 +7,14 @@ from toardb.variables.models import Variable
from toardb.contacts.models import Person, Organisation
from toardb.auth_user.models import AuthUser
# Required imports 'create_test_database'
-from .test_base import (
+from toardb.test_base import (
client,
get_test_db,
create_test_database,
url,
+ get_test_engine,
test_db_session as db,
)
-from .test_base import _db_conn
class TestApps:
def setup(self):
@@ -27,6 +27,8 @@ class TestApps:
"""
@pytest.fixture(autouse=True)
def setup_db_data(self, db):
+ _db_conn = get_test_engine()
+ print(_db_conn)
# id_seq will not be reset automatically between tests!
fake_conn = _db_conn.raw_connection()
fake_cur = fake_conn.cursor()
@@ -44,11 +46,11 @@ class TestApps:
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE stationmeta_annotations_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_docs_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_doc_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_images_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_image_id_seq RESTART WITH 1")
fake_conn.commit()
- fake_cur.execute("ALTER SEQUENCE stationmeta_aux_urls_id_seq RESTART WITH 1")
+ fake_cur.execute("ALTER SEQUENCE stationmeta_aux_url_id_seq RESTART WITH 1")
fake_conn.commit()
fake_cur.execute("ALTER SEQUENCE persons_id_seq RESTART WITH 1")
fake_conn.commit()
@@ -119,9 +121,11 @@ class TestApps:
def test_get_timeseries(self, client, db):
+ print("==============Client: ================", client.base_url)
response = client.get("/timeseries/")
expected_status_code = 200
assert response.status_code == expected_status_code
+ print("I got: ", response.json())
expected_resp = [{'id': 1, 'label': 'CMA', 'order': 1, 'access_rights': 0,
'sampling_frequency': 0, 'aggregation': 0,
'data_start_date': '2003-09-07T15:30:00+02:00', 'data_end_date': '2016-12-31T14:30:00+01:00',
diff --git a/toardb/timeseries/timeseries.py b/toardb/timeseries/timeseries.py
index de1819b099dfee8c05097e3993f96031626813ff..617bd82da0dd98fecb239410c7bedc32f45b8199 100644
--- a/toardb/timeseries/timeseries.py
+++ b/toardb/timeseries/timeseries.py
@@ -6,20 +6,10 @@ from typing import List
from fastapi import APIRouter, Depends, HTTPException, Body
from sqlalchemy.orm import Session
from . import crud, schemas
-from toardb.utils.database import ToarDbSession
+from toardb.utils.database import ToarDbSession, get_db
router = APIRouter()
-# Dependency
-def get_db():
- try:
- db = ToarDbSession()
- yield db
- finally:
- db.close()
-
-
-
# plain views to post and get timeseries
#get all entries of table timeseries
diff --git a/toardb/utils/database.py b/toardb/utils/database.py
index b31d57dcd7e499c4695528c859a6599315b2c75b..d31e48577dfc7b55a8adfd2dd9ccd04c590fb1a2 100644
--- a/toardb/utils/database.py
+++ b/toardb/utils/database.py
@@ -9,3 +9,16 @@ DATABASE_URL = "postgresql://toaradmin:toar2@localhost:5432/toardb"
engine = create_engine(DATABASE_URL)
ToarDbSession = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+
+# Dependency
+def get_engine():
+ assert engine is not None
+ return engine
+
+# Dependency
+def get_db():
+ try:
+ db = ToarDbSession()
+ yield db
+ finally:
+ db.close()
diff --git a/toardb/variables/models.py b/toardb/variables/models.py
index 06a6511c165a7e825a05fade2d81cde7387746ba..22315aac47a6e519bf9c0b52c003f63d52b6ff37 100644
--- a/toardb/variables/models.py
+++ b/toardb/variables/models.py
@@ -1,11 +1,12 @@
# coding: utf-8
-from sqlalchemy import ARRAY, BigInteger, Boolean, CheckConstraint, Column, DateTime, Float, ForeignKey, Index, Integer, SmallInteger, String, Text, UniqueConstraint, text
+from sqlalchemy import Column, Integer, String, Sequence
from sqlalchemy.orm import relationship
from sqlalchemy.sql.sqltypes import NullType
from sqlalchemy.dialects.postgresql import JSONB
from toardb.base import Base
+VARIABLES_ID_SEQ = Sequence('variables_id_seq') # define sequence explicitly
class Variable(Base):
""" Table "public.variables"
@@ -35,7 +36,7 @@ class Variable(Base):
"""
__tablename__ = 'variables'
- id = Column(Integer, primary_key=True, server_default=text("nextval('variables_id_seq'::regclass)"))
+ id = Column(Integer, VARIABLES_ID_SEQ, primary_key=True, server_default=VARIABLES_ID_SEQ.next_value())
name = Column(String(32), nullable=False, unique=True)
longname = Column(String(128), nullable=False)
displayname = Column(String(128), nullable=False)
diff --git a/toardb/variables/test_variables.py b/toardb/variables/test_variables.py
index c58b2d03aa46c9cd082109a82708536fa1973839..538428d52c6ee24ebce023aee32aee98ee49269b 100644
--- a/toardb/variables/test_variables.py
+++ b/toardb/variables/test_variables.py
@@ -2,14 +2,14 @@ import pytest
import json
from .models import Variable
# Required imports 'create_test_database'
-from .test_base import (
+from toardb.test_base import (
client,
get_test_db,
create_test_database,
url,
+ get_test_engine,
test_db_session as db,
)
-from .test_base import _db_conn
class TestApps:
def setup(self):
@@ -23,6 +23,7 @@ class TestApps:
@pytest.fixture(autouse=True)
def setup_db_data(self, db):
# id_seq will not be reset automatically between tests!
+ _db_conn = get_test_engine()
fake_conn = _db_conn.raw_connection()
fake_cur = fake_conn.cursor()
fake_cur.execute("ALTER SEQUENCE variables_id_seq RESTART WITH 1")
diff --git a/toardb/variables/variables.py b/toardb/variables/variables.py
index dbc633c6a5db77dfc12ded2044edd5f260149c1a..55ddc2bc7d2cf760a2b585fb787bc46cce9b1a0e 100644
--- a/toardb/variables/variables.py
+++ b/toardb/variables/variables.py
@@ -6,19 +6,10 @@ from typing import List
from fastapi import APIRouter, Depends, HTTPException
from sqlalchemy.orm import Session
from toardb.variables import crud, schemas
-from toardb.utils.database import ToarDbSession
+from toardb.utils.database import ToarDbSession, get_db
router= APIRouter()
-# Dependency
-def get_db():
- try:
- db = ToarDbSession()
- yield db
- finally:
- db.close()
-
-
# plain views to post and get variables
@router.post('/variables/', response_model=schemas.Variable)
def create_variable(variable: schemas.VariableCreate, db: Session = Depends(get_db)):