#1 - Update and create new unit tests

database/tests/test_metadata.py

@@ -11,42 +11,72 @@
 limitations under the License.
 """
 
+import sqlalchemy as sa
+
 from aiohttp.test_utils import unittest_run_loop
-from database.job import save_job
-from database.metadata import metadata, search_metadata
+from database.metadata import metadata, search_metadata, update_metadata
+from database.models import Job
 from database.tests.test_base import DBTestCase
 
 
-class SaveMetadataTestCase(DBTestCase):
+class MetadataTestCase(DBTestCase):
     """
     Run this test with the following command:
-    ENVIRONMENT=TEST python -m unittest database.tests.test_jobs.SaveMetadataTestCase
+    ENVIRONMENT=TEST python -m unittest database.tests.test_jobs.MetadataTestCase
     """
     async def setUpAsync(self):
         await super().setUpAsync()
 
+        async with self.app['engine'].acquire() as connection:
+            await connection.execute(Job.insert().values(job_id='foo.bar'))
+            await connection.execute(Job.insert().values(job_id='urs001'))
+
+            results = [
+                {"job_id": "foo.bar", "name": "rnacentral", "primary_id": "urs001"},
+                {"job_id": "urs001", "name": "rnacentral", "primary_id": None},
+                {"job_id": "foo.bar", "name": "test", "primary_id": None},
+            ]
+            await metadata(self.app['engine'], results=results)
+
+    async def tearDownAsync(self):
+        async with self.app['engine'].acquire() as connection:
+            await connection.execute('DELETE FROM database')
+            await connection.execute('DELETE FROM result')
+            await connection.execute('DELETE FROM job')
+
+        await super().tearDownAsync()
+
     @unittest_run_loop
-    async def test_save_job(self):
-        job_id = await save_job(
-            self.app['engine'],
-            job_id="foo.bar"
-        )
-        urs = await save_job(
-            self.app['engine'],
-            job_id="urs001"
-        )
-        results = [
-            {"job_id": job_id, "name": "rnacentral", "primary_id": urs},
-            {"job_id": urs, "name": "rnacentral", "primary_id": None},
-            {"job_id": job_id, "name": "test", "primary_id": None},
-        ]
-        await metadata(self.app['engine'], results=results)
-
-        find_metadata_1 = await search_metadata(self.app['engine'], job_id, "test", None)
+    async def test_find_job_id_with_expert_db(self):
+        find_metadata_1 = await search_metadata(self.app['engine'], "foo.bar", "test", None)
         assert find_metadata_1 is not None
 
-        find_metadata_2 = await search_metadata(self.app['engine'], job_id, "rnacentral", urs)
+    @unittest_run_loop
+    async def test_find_job_id_with_rnacentral(self):
+        find_metadata_2 = await search_metadata(self.app['engine'], "foo.bar", "rnacentral", 'urs001')
         assert find_metadata_2 is not None
 
-        find_metadata_3 = await search_metadata(self.app['engine'], urs, "rnacentral", None)
+    @unittest_run_loop
+    async def test_find_urs(self):
+        find_metadata_3 = await search_metadata(self.app['engine'], "urs001", "rnacentral", None)
         assert find_metadata_3 is not None
+
+    @unittest_run_loop
+    async def test_wrong_job_id(self):
+        wrong_job = await search_metadata(self.app['engine'], "wrong_job", "rnacentral", None)
+        assert wrong_job is None
+
+    @unittest_run_loop
+    async def test_update_manually_annotated(self):
+        await update_metadata(self.app['engine'], "foo.bar", "urs001", "rnacentral")
+
+        async with self.app['engine'].acquire() as connection:
+            query = sa.text('''
+                SELECT manually_annotated
+                FROM database
+                WHERE job_id=:job_id AND primary_id=:primary_id AND name=:name
+            ''')
+
+            async for row in await connection.execute(query, job_id="foo.bar", primary_id="urs001", name="rnacentral"):
+                result = row.manually_annotated
+                assert result is True