Dunitz/db setup (#1619)

* initial database setup

server/test/fixtures/database/__init__.py

@@ -0,0 +1,87 @@
+import string
+import random
+
+
+from sqlalchemy import func
+
+from server.db.cellxgene_orm import CellxGeneUser, CellxGeneDataset, Annotation, Base
+from server.db.create_db import create_db
+from server.db.db_utils import DbUtils
+
+
+class TestDatabase:
+    def __init__(self):
+        local_db_uri = "postgresql://postgres:test_pw@localhost:5432"
+        create_db(local_db_uri)
+        self.db = DbUtils(local_db_uri)
+        self._populate_test_data()
+        self._populate_test_data_many()
+
+    def _populate_test_data(self):
+        self._create_test_user()
+        self._create_test_dataset()
+        self._create_test_annotation()
+
+    def _populate_test_data_many(self):
+        self._create_test_users()
+        self._create_test_datasets()
+        self._create_test_annotations()
+
+    def _create_test_user(self):
+        user = CellxGeneUser(id="test_user_id")
+        self.db.session.add(user)
+        self.db.session.commit()
+
+    def _create_test_dataset(self):
+        dataset = CellxGeneDataset(
+            id="test_dataset_id",
+            name="test_dataset",
+        )
+        self.db.session.add(dataset)
+        self.db.session.commit()
+
+    def _create_test_annotation(self):
+        annotation = Annotation(
+            id="test_annotation_id",
+            tiledb_uri="tiledb_uri",
+            user_id="test_user_id",
+            dataset_id="test_dataset_id"
+        )
+        self.db.session.add(annotation)
+        self.db.session.commit()
+
+    @staticmethod
+    def get_random_string():
+        letters = string.ascii_lowercase
+        return ''.join(random.choice(letters) for i in range(12))
+
+    def _create_test_users(self, user_count: int = 10):
+        users = []
+        for i in range(user_count):
+            users.append(CellxGeneUser(id=self.get_random_string()))
+        self.db.session.add_all(users)
+        self.db.session.commit()
+
+    def _create_test_datasets(self, dataset_count: int = 10):
+        datasets = []
+        for i in range(dataset_count):
+            datasets.append(CellxGeneDataset(id=self.get_random_string(), name=self.get_random_string()))
+        self.db.session.add_all(datasets)
+        self.db.session.commit()
+
+    def order_by_random(self, table: Base):
+        return self.db.session.query(table).order_by(func.random()).first()
+
+    def _create_test_annotations(self, annotation_count: int = 10):
+        annotations = []
+        for i in range(annotation_count):
+            dataset = self.order_by_random(CellxGeneDataset)
+            user = self.order_by_random(CellxGeneUser)
+            annotations.append(Annotation(
+                id=self.get_random_string(),
+                tiledb_uri=self.get_random_string(),
+                user_id=user.id,
+                dataset_id=dataset.id
+            ))
+        self.db.session.add_all(annotations)
+        self.db.session.commit()

server/test/test_database/test_database.py

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+import unittest
+from server.db.cellxgene_orm import CellxGeneUser, CellxGeneDataset, Annotation
+from server.db.db_utils import DbUtils
+from server.test.fixtures.database import TestDatabase
+
+
+class AppConfigTest(unittest.TestCase):
+    db = DbUtils("postgresql://postgres:test_pw@localhost:5432")
+
+    @classmethod
+    def setUpClass(cls) -> None:
+        TestDatabase()
+
+    @classmethod
+    def tearDownClass(cls) -> None:
+        del cls.db
+
+    def test_user_creation(self):
+        one_user = self.db.get(table=CellxGeneUser, entity_id='test_user_id')
+        self.assertEqual(one_user.id, 'test_user_id')
+        user_count = self.db.session.query(CellxGeneUser).count()
+        self.assertGreater(user_count, 10)
+
+    def test_dataset_creation(self):
+        one_dataset = self.db.get(table=CellxGeneDataset, entity_id='test_dataset_id')
+        self.assertEqual(one_dataset.id, 'test_dataset_id')
+        dataset_count = self.db.session.query(CellxGeneDataset).count()
+        self.assertGreater(dataset_count, 10)
+
+    def test_annotation_creation(self):
+        one_annotation = self.db.get(table=Annotation, entity_id='test_annotation_id')
+        self.assertEqual(one_annotation.id, 'test_annotation_id')
+        annotation_count = self.db.session.query(Annotation).count()
+        self.assertGreater(annotation_count, 10)