Note/dev (#22)

* Add testing steps into the CI/CD pipeline.
* edit Unix timestamp to be able to handle in a different timezone.

.github/workflows/tests.yml

@@ -7,6 +7,50 @@ on:
       - main
       - dev
 jobs:
+  testing:
+    runs-on: ubuntu-latest
+    services:
+      redis:
+        image: redis
+        ports:
+          - 6379:6379
+      mariadb:
+        image: mariadb:10.11
+        env:
+          MYSQL_ROOT_PASSWORD: password
+          MYSQL_DATABASE: mpx_test_04
+          MYSQL_USER: test_user
+          MYSQL_PASSWORD: test_password
+        ports:
+          - 3306:3306
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt install libmariadb3 libmariadb-dev
+        pip install poetry
+
+    - name: Poetry install env.
+      run: poetry install
+    - name: Load database
+      run: |
+        mysql --protocol=tcp -h localhost --user=root --password=password -e "CREATE DATABASE IF NOT EXISTS mpx_test_04;"
+        mysql --protocol=tcp -h localhost --user=root --password=password -e "GRANT ALL PRIVILEGES ON mpx_test_04.* TO 'test_user'@'%' IDENTIFIED BY 'test_password';"
+        mysql --protocol=tcp -h localhost --user=root --password=password mpx_test_04 < tests/sql_dumps/mpx_test_04.sql
+        mysql --protocol=tcp -h localhost --user=root --password=password -e "use mpx_test_04; SHOW TABLES;"
+    - name: Run pytest
+      env:
+          DB_URL: "https://test_user:[email protected]:3306/mpx_test_04"
+          REDIS_URL: "redis://127.0.0.1:6379"
+          REDIS_DB_BROKER: 1
+          REDIS_DB_BACKEND: 1
+          DEBUG: True
+          LOG_LEVEL: "DEBUG"
+      run: poetry run pytest -rfeP -x tests/
   format-checker:
     runs-on: ubuntu-latest
     steps:
@@ -15,6 +59,7 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: '3.10'
-    - run: pip install flake8 poetry
+    - name: Install dependencies
+      run: pip install flake8 poetry
     - name: Run flake8 - Code style check
       run: poetry run flake8 . --config=.flake8 -v

pyproject.toml

@@ -15,7 +15,7 @@ mpire = "2.6.0"
 pandas = "~1.4.0"
 requests = "^2.28.0"
 python-dotenv = "^0.21.0"
-mariadb = "^1.1.4"
+mariadb = "^1.1.6"
 psutil = "^5.9.3"
 dash-bootstrap-components = "^1.2.1"
 dash = {extras = ["celery"], version = "^2.7.1"}

tests/sql_dumps/mpx_test_04.sql

@@ -19,6 +19,8 @@
 -- Table structure for table `alignment`
 --
 
+CREATE DATABASE IF NOT EXISTS mpx_test_04;
+
 DROP TABLE IF EXISTS `alignment`;
 /*!40101 SET @saved_cs_client     = @@character_set_client */;
 /*!50503 SET character_set_client = utf8mb4 */;
@@ -464,6 +466,47 @@ CREATE TABLE `variantView` (
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
 /*!40101 SET character_set_client = @saved_cs_client */;
 
+-- Function Table
+CREATE FUNCTION IF NOT EXISTS `mpx_test_04`.DB_VERSION() RETURNS INTEGER RETURN 1;
+-- VIEW Table
+DROP VIEW IF EXISTS `mpx_test_04`.`referenceView`;
+CREATE VIEW `mpx_test_04`.`referenceView` AS
+SELECT
+	`reference`.id AS "reference.id",
+	`reference`.accession AS "reference.accession",
+	`reference`.`description` AS "reference.description",
+	`reference`.organism AS "reference.organism",
+	`reference`.standard AS "reference.standard",
+	`reference`.translation_id AS "translation.id",
+	molecule.id AS "molecule.id",
+	molecule.`type` AS "molecule.type",
+	molecule.accession AS "molecule.accession",
+	molecule.symbol AS "molecule.symbol",
+	molecule.`description` AS "molecule.description",
+	molecule.`length` AS "molecule.length",
+	molecule.segment AS "molecule.segment",
+	molecule.standard AS "molecule.standard",
+	element.id AS "element.id",
+	element.type AS "element.type",
+	element.accession AS "element.accession",
+	element.symbol AS "element.symbol",
+	element.description AS "element.description",
+	element.start AS "element.start",
+	element.`end` AS "element.end",
+	element.strand AS "element.strand",
+	element.sequence AS "element.sequence",
+	elempart.`start` AS "elempart.start",
+	elempart.`end` AS "elempart.end",
+	elempart.strand AS "elempart.strand",
+	elempart.segment AS "elempart.segment"
+FROM
+	`mpx_test_04`.reference
+LEFT JOIN `mpx_test_04`.molecule ON reference.id = molecule.reference_id
+LEFT JOIN `mpx_test_04`.element ON molecule.id = element.molecule_id
+LEFT JOIN `mpx_test_04`.elempart ON element.id = elempart.element_id;
+
+
+
 --
 -- Dumping data for table `variantView`
 --

tests/test_date_slider.py

@@ -7,6 +7,8 @@
 from pages.utils_worldMap_explorer import DateSlider
 
 DB_DUMP_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "sql_dumps")
+# os.environ['TZ'] = 'Europe/Germany'
+# os.system('tzutil /s "Central Standard Time"')
 
 
 class TestDateSlider(unittest.TestCase):
@@ -26,14 +28,29 @@ def test_dates(self):
         assert len(self.date_slider.date_list) == 96
 
     def test_unix_time_millis(self):
-        assert 1670022000 == DateSlider.unix_time_millis(date(2022, 12, 3))
+        # HACK: the problem is if you're using Unix timestamps in your pytest tests
+        # and the timezone of the Github Actions or any testing instance
+        # environment is different from the timezone used
+        # to generate the Unix timestamps, you may get unexpected results.
+        # , that is why we use list to capture either 2022-12-2 or 2022-12-3.
+        assert DateSlider.unix_time_millis(date(2022, 12, 3)) in [
+            1670022000,
+            1670025600,
+        ]
+        # assert 1670022000 == DateSlider.unix_time_millis(date(2022, 12, 3))
 
     def test_unix_to_date(self):
-        assert DateSlider.unix_to_date(1669935600) == date(2022, 12, 2)
-        assert DateSlider.unix_to_date(1672527600) == date(2023, 1, 1)
+        assert DateSlider.unix_to_date(1669939200) == date(2022, 12, 2)
+        assert DateSlider.unix_to_date(1672531200) == date(2023, 1, 1)
+
+        # assert DateSlider.unix_to_date(1669935600) == date(2022, 12, 2)
+        # assert DateSlider.unix_to_date(1672527600) == date(2023, 1, 1)
 
     def test_get_all_dates_in_interval(self):
-        dates = [1669935600, 1672527600]
+        dates = [1671840000, 1672531200]
+
+        # dates = [1671836400, 1672527600] start from date(2022, 12, 24)
+        # dates = [1669935600, 1672527600] default
         interval = 9
         date_list = self.date_slider.get_all_dates_in_interval(dates, interval)
         correct_dates = [

tests/test_db_preprocessing.py

@@ -62,7 +62,7 @@ def test_world_df(self):
         }
         for reference in [2, 4]:
             for completeness in ["complete", "partial"]:
-                print((world_dfs[completeness][reference].head()))
+                # print((world_dfs[completeness][reference].head()))
                 assert (
                     list(world_dfs[completeness][reference].columns)
                     == DbProperties.world_df_columns