Fix SSL-disabled OpenSearch tests

abcd/frontends/commandline/commands.py

@@ -21,6 +21,7 @@ def login(*, config, name, url, disable_ssl=False, **kwargs):
     info = db.info()
 
     config["url"] = url
+    config["use_ssl"] = not disable_ssl
     config.save()
 
     print("Successfully connected to the database!")

abcd/frontends/commandline/decorators.py

@@ -20,12 +20,17 @@ def init_db(func):
     @functools.wraps(func)
     def wrapper(*args, config, **kwargs):
         url = config.get("url", None)
+        use_ssl = config.get("use_ssl", None)
 
         if url is None:
             print("Please use abcd login first!")
             exit(1)
 
-        db = ABCD.from_url(url=url)
+        if use_ssl is None:
+            print("use_ssl has not been saved. Please login again")
+            exit(1)
+
+        db = ABCD.from_url(url=url, use_ssl=use_ssl)
 
         # TODO: AST.from_string() ?!
         # TODO: better ast optimisation

tests/__init__.py

@@ -1,9 +1,11 @@
 import unittest
 import logging
-# from tests.parsers import ParsingQueries, ParsingExtras
-# from tests.database import MongoMock, OpenSearchMock
-# from tests.properties import PropertiesTests
-# from tests.opensearch import OpenSearch
+
+from tests.parsers import ParsingQueries, ParsingExtras
+from tests.properties import PropertiesTests
+from tests.mongo_mock import MongoMock
+from tests.opensearch_mock import OpenSearchMock
+from tests.opensearch import OpenSearch
 from tests.cli import CLI
 
 if __name__ == "__main__":

tests/cli.py

@@ -19,11 +19,15 @@ def setUpClass(cls):
         cls.security_enabled = os.getenv("security_enabled") == "true"
         cls.port = int(os.environ["port"])
         cls.host = "localhost"
+
         logging.basicConfig(level=logging.INFO)
+
         url = f"opensearch://admin:admin@{cls.host}:{cls.port}"
+        if not cls.security_enabled:
+            url += " --disable_ssl"
         try:
             os.system(f"abcd login {url}")
-        except ConnectionError or ConnectionResetError:
+        except (ConnectionError, ConnectionResetError):
             sleep(10)
             os.system(f"abcd login {url}")
 

tests/mongo_mock.py

@@ -0,0 +1,52 @@
+from io import StringIO
+import logging
+import unittest
+
+from ase.io import read
+from ase.atoms import Atoms
+import mongomock
+
+from abcd import ABCD
+
+
+class MongoMock(unittest.TestCase):
+    @classmethod
+    @mongomock.patch(servers=(("localhost", 27017),))
+    def setUpClass(cls):
+        logging.basicConfig(level=logging.INFO)
+        url = "mongodb://localhost"
+        abcd = ABCD.from_url(url)
+        abcd.print_info()
+
+        cls.abcd = abcd
+
+    @classmethod
+    def tearDownClass(cls):
+        cls.abcd.destroy()
+
+    def test_thing(self):
+        print(self.abcd.info())
+
+    def test_push(self):
+        xyz = StringIO(
+            """2
+            Properties=species:S:1:pos:R:3 s="sadf" _vtk_test="t _ e s t" pbc="F F F"
+            Si       0.00000000       0.00000000       0.00000000
+            Si       0.00000000       0.00000000       0.00000000
+            """
+        )
+
+        atoms = read(xyz, format="extxyz")
+        assert isinstance(atoms, Atoms)
+        atoms.set_cell([1, 1, 1])
+
+        self.abcd.destroy()
+        self.abcd.push(atoms)
+        new = list(self.abcd.get_atoms())[0]
+
+        assert atoms == new
+        self.abcd.destroy()
+
+
+if __name__ == "__main__":
+    unittest.main(verbosity=1, exit=False)

tests/opensearch.py

@@ -1,14 +1,16 @@
-import unittest
-from abcd import ABCD
+from io import StringIO
 import logging
 import os
 from time import sleep
-from abcd.backends.atoms_opensearch import OpenSearchDatabase
-from opensearchpy.exceptions import ConnectionError
-from io import StringIO
-from ase.io import read
+import unittest
+
 from ase.atoms import Atoms
-from abcd.backends.atoms_opensearch import AtomsModel
+from ase.io import read
+from opensearchpy.exceptions import ConnectionError
+
+from abcd import ABCD
+from abcd.backends.atoms_opensearch import AtomsModel, OpenSearchDatabase
+
 
 class OpenSearch(unittest.TestCase):
     """
@@ -36,7 +38,7 @@ def setUpClass(cls):
                 analyse_schema=False,
                 use_ssl=cls.security_enabled,
             )
-        except ConnectionError or ConnectionResetError:
+        except (ConnectionError, ConnectionResetError):
             sleep(10)
             abcd = ABCD.from_url(
                 url,
@@ -103,7 +105,6 @@ def test_destroy(self):
 
         self.abcd.destroy()
         self.assertFalse(self.abcd.client.indices.exists("test_index"))
-        return
 
     def test_create(self):
         """
@@ -165,7 +166,6 @@ def test_delete(self):
         self.assertTrue(self.abcd.client.indices.exists("test_index"))
         self.abcd.refresh()
         self.assertEqual(self.abcd.count(), 0)
-        return
 
     def test_bulk(self):
         """

tests/database.py → tests/opensearch_mock.py

@@ -1,52 +1,16 @@
+from importlib import reload
+from io import StringIO
+import logging
+import os
 import unittest
-import mongomock
+
+from ase.atoms import Atoms
+from ase.io import read
 from openmock import openmock
 
 from abcd import ABCD
-import logging
-
-
-class MongoMock(unittest.TestCase):
-    @classmethod
-    @mongomock.patch(servers=(("localhost", 27017),))
-    def setUpClass(cls):
-        logging.basicConfig(level=logging.INFO)
-        url = "mongodb://localhost"
-        abcd = ABCD.from_url(url)
-        abcd.print_info()
-
-        cls.abcd = abcd
-
-    @classmethod
-    def tearDownClass(cls):
-        cls.abcd.destroy()
-
-    def test_thing(self):
-        print(self.abcd.info())
-
-    def test_push(self):
-        from io import StringIO
-        from ase.io import read
-        from ase.atoms import Atoms
-
-        xyz = StringIO(
-            """2
-            Properties=species:S:1:pos:R:3 s="sadf" _vtk_test="t _ e s t" pbc="F F F"
-            Si       0.00000000       0.00000000       0.00000000
-            Si       0.00000000       0.00000000       0.00000000
-            """
-        )
-
-        atoms = read(xyz, format="extxyz")
-        assert isinstance(atoms, Atoms)
-        atoms.set_cell([1, 1, 1])
-
-        self.abcd.destroy()
-        self.abcd.push(atoms)
-        new = list(self.abcd.get_atoms())[0]
-
-        assert atoms == new
-        self.abcd.destroy()
+from abcd.backends import atoms_opensearch
+from abcd.backends.atoms_opensearch import AtomsModel
 
 
 class OpenSearchMock(unittest.TestCase):
@@ -60,10 +24,18 @@ def setUpClass(cls):
         """
         Set up database connection.
         """
+        reload(atoms_opensearch)
         from abcd.backends.atoms_opensearch import OpenSearchDatabase
 
+        if "port" in os.environ:
+            cls.port = int(os.environ["port"])
+        else:
+            cls.port = 9200
+        cls.host = "localhost"
+
         logging.basicConfig(level=logging.INFO)
-        url = "opensearch://admin:admin@localhost:9200"
+
+        url = f"opensearch://admin:admin@{cls.host}:{cls.port}"
         abcd = ABCD.from_url(url, index_name="test_index", analyse_schema=False)
         assert isinstance(abcd, OpenSearchDatabase)
         cls.abcd = abcd
@@ -82,7 +54,6 @@ def test_destroy(self):
         self.assertTrue(self.abcd.client.indices.exists("test_index"))
         self.abcd.destroy()
         self.assertFalse(self.abcd.client.indices.exists("test_index"))
-        return
 
     def test_create(self):
         """
@@ -97,11 +68,6 @@ def test_push(self):
         """
         Test pushing atoms objects to database individually.
         """
-        from io import StringIO
-        from ase.io import read
-        from ase.atoms import Atoms
-        from abcd.backends.atoms_opensearch import AtomsModel
-
         self.abcd.destroy()
         self.abcd.create()
         xyz_1 = StringIO(
@@ -139,11 +105,6 @@ def test_bulk(self):
         """
         Test pushing atoms object to database together.
         """
-        from io import StringIO
-        from ase.io import read
-        from ase.atoms import Atoms
-        from abcd.backends.atoms_opensearch import AtomsModel
-
         self.abcd.destroy()
         self.abcd.create()
         xyz_1 = StringIO(
@@ -190,10 +151,6 @@ def test_count(self):
         """
         Test counting the number of documents in the database.
         """
-        from io import StringIO
-        from ase.io import read
-        from ase.atoms import Atoms
-
         self.abcd.destroy()
         self.abcd.create()
         xyz = StringIO(

tests/parsers.py

@@ -188,7 +188,7 @@ def test_operators(self):
             ('string = "some string"', {}),
             ('regexp ~ ".*H"', {}),
         )
-        for string, expected in s:
+        for string, _ in s:
             with self.subTest(string=string):
                 self.parser.parse(string)
 
@@ -200,7 +200,7 @@ def test_combination(self):
             ("aa and bb > 23 and bb > 23 and bb > 23 ", {}),
             ("aa and bb > 23.54 or 22 in cc and dd", {}),
         )
-        for string, expected in s:
+        for string, _ in s:
             with self.subTest(string=string):
                 self.parser.parse(string)
 
@@ -213,7 +213,7 @@ def test_expressions(self):
             ("all(aa) > 3", {}),
             ("any(aa) > 3", {}),
         )
-        for string, expected in s:
+        for string, _ in s:
             with self.subTest(string=string):
                 self.parser.parse(string)
 

tests/properties.py

@@ -1,4 +1,8 @@
+import os
 import unittest
+
+from pandas import DataFrame
+
 from abcd.backends.atoms_properties import Properties
 
 
@@ -10,18 +14,14 @@ def setUpClass(cls):
         """
         Load example data file.
         """
-        import os
-
         class_path = os.path.normpath(os.path.abspath(__file__))
-        data_file = os.path.dirname(class_path) + "/examples.csv"
+        data_file = os.path.dirname(class_path) + "/data/examples.csv"
         cls.property = Properties(data_file)
 
     def test_dataframe(self):
         """
         Test data correctly stored in pandas DataFrame.
         """
-        from pandas import DataFrame
-
         assert isinstance(self.property.df, DataFrame)
         assert len(self.property.df) == 3