General housekeeping

cyllab · Jul 10, 2022 · 9ede6b6 · 9ede6b6
1 parent ea9c7c3
commit 9ede6b6
Show file tree

Hide file tree

Showing 32 changed files with 9,763 additions and 22,199 deletions.
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -20,6 +20,7 @@ services:
                         - ./backups:/calcus/backups
                         - ./logs:/calcus/logs
                         - ./frontend/migrations:/calcus/frontend/migrations
+                        - ./scripts:/calcus/scripts
                 links:
                         - redis
                 env_file:

diff --git a/frontend/calcusliveserver.py b/frontend/calcusliveserver.py
diff --git a/frontend/templates/frontend/base.html b/frontend/templates/frontend/base.html
@@ -200,7 +200,7 @@
 
 
 					{% if user.profile.group != None %}
-					<div class="navbar-item has-dropdown is-hoverable">
+					<div class="navbar-item has-dropdown is-hoverable" id="navbar_group">
 						<a class="navbar-link">Research Group</a>
 						<div class="navbar-dropdown">
 							<a class="navbar-item" href="/projects/{{ user.profile.group.PI.username }}">{{ user.profile.group.PI.username }}</a>
@@ -211,7 +211,7 @@
 					</div>
 					{% endif %}
 					{% if user.profile.clusteraccess_owner.count > 0 %}
-					<div class="navbar-item has-dropdown is-hoverable">
+					<div class="navbar-item has-dropdown is-hoverable" id="navbar_accesses">
 						<a class="navbar-link">Cluster Accesses</a>
 						<div class="navbar-dropdown">
 							{% for a in user.profile.clusteraccess_owner.all %}

diff --git a/frontend/test_cluster.py b/frontend/test_cluster.py
@@ -95,15 +95,16 @@ def run_daemon(self):
 
     def test_setup(self):
         self.setup_cluster()
-        msg = self.driver.find_element_by_id("test_msg").text
+        msg = self.driver.find_element(By.ID, "test_msg").text
         self.assertEqual(msg, "Connected")
 
     def setup_cluster(self):
         self.lget("/profile")
 
         try:
-            access = self.driver.find_element_by_css_selector(
-                "#owned_accesses > center > table > tbody > tr > th:nth-child(3) > a"
+            access = self.driver.find_element(
+                By.CSS_SELECTOR,
+                "#owned_accesses > center > table > tbody > tr > th:nth-child(3) > a",
             )
         except selenium.common.exceptions.NoSuchElementException:
             pass
@@ -134,7 +135,7 @@ def test_delete_access(self):
         while not main_window_handle:
             main_window_handle = self.driver.current_window_handle
 
-        delete_access = self.driver.find_element_by_id("delete_access_button")
+        delete_access = self.driver.find_element(By.ID, "delete_access_button")
         delete_access.click()
 
         alert = Alert(self.driver)
@@ -151,25 +152,25 @@ def test_delete_access(self):
     def test_cluster_settings(self):
         self.lget("/profile")
 
-        adress = self.driver.find_element_by_name("cluster_address")
+        adress = self.driver.find_element(By.NAME, "cluster_address")
         adress.send_keys("localhost")
 
-        username = self.driver.find_element_by_name("cluster_username")
+        username = self.driver.find_element(By.NAME, "cluster_username")
         username.send_keys("cluster")
 
-        pal = self.driver.find_element_by_name("cluster_cores")
+        pal = self.driver.find_element(By.NAME, "cluster_cores")
         pal.clear()
         pal.send_keys("8")
 
-        memory = self.driver.find_element_by_name("cluster_memory")
+        memory = self.driver.find_element(By.NAME, "cluster_memory")
         memory.clear()
         memory.send_keys("10000")
 
-        password = self.driver.find_element_by_name("cluster_password")
+        password = self.driver.find_element(By.NAME, "cluster_password")
         password.clear()
         password.send_keys("Selenium")
 
-        self.driver.find_element_by_id("add_access_button").click()
+        self.driver.find_element(By.ID, "add_access_button").click()
         element = WebDriverWait(self.driver, 10).until(
             EC.presence_of_element_located((By.ID, "public_key_area"))
         )
@@ -184,25 +185,25 @@ def test_cluster_settings(self):
     def test_cluster_settings2(self):
         self.lget("/profile")
 
-        adress = self.driver.find_element_by_name("cluster_address")
+        adress = self.driver.find_element(By.NAME, "cluster_address")
         adress.send_keys("localhost")
 
-        username = self.driver.find_element_by_name("cluster_username")
+        username = self.driver.find_element(By.NAME, "cluster_username")
         username.send_keys("cluster")
 
-        pal = self.driver.find_element_by_name("cluster_cores")
+        pal = self.driver.find_element(By.NAME, "cluster_cores")
         pal.clear()
         pal.send_keys("24")
 
-        memory = self.driver.find_element_by_name("cluster_memory")
+        memory = self.driver.find_element(By.NAME, "cluster_memory")
         memory.clear()
         memory.send_keys("31000")
 
-        password = self.driver.find_element_by_name("cluster_password")
+        password = self.driver.find_element(By.NAME, "cluster_password")
         password.clear()
         password.send_keys("Selenium")
 
-        self.driver.find_element_by_id("add_access_button").click()
+        self.driver.find_element(By.ID, "add_access_button").click()
         element = WebDriverWait(self.driver, 10).until(
             EC.presence_of_element_located((By.ID, "public_key_area"))
         )
@@ -216,20 +217,21 @@ def test_cluster_settings2(self):
 
     def test_connection_gui(self):
         self.setup_cluster()
-        msg = self.driver.find_element_by_id("test_msg").text
+        msg = self.driver.find_element(By.ID, "test_msg").text
         self.assertEqual(msg, "Connected")
 
         self.lget("/profile/")
-        manage = self.driver.find_element_by_css_selector(
-            "#owned_accesses > center > table > tbody > tr > th:nth-child(3) > a"
+        manage = self.driver.find_element(
+            By.CSS_SELECTOR,
+            "#owned_accesses > center > table > tbody > tr > th:nth-child(3) > a",
         )
         manage.send_keys(Keys.RETURN)
 
         element = WebDriverWait(self.driver, 10).until(
             EC.text_to_be_present_in_element((By.ID, "status_box"), "Connected")
         )
         self.assertNotEqual(
-            self.driver.find_element_by_id("status_box").text.find("Connected"), -1
+            self.driver.find_element(By.ID, "status_box").text.find("Connected"), -1
         )
 
     def test_autoselect_resource_remote(self):
@@ -250,7 +252,9 @@ def test_autoselect_resource_remote(self):
 
         self.lget("/launch/")
 
-        resources = self.driver.find_elements_by_css_selector("#calc_resource > option")
+        resources = self.driver.find_elements(
+            By.CSS_SELECTOR, "#calc_resource > option"
+        )
         self.assertEqual(len(resources), 2)
         self.assertEqual(resources[0].text, "Local")
         self.assertTrue(resources[0].is_selected())
@@ -260,7 +264,9 @@ def test_autoselect_resource_remote(self):
 
         self.calc_input_params(params)
 
-        resources = self.driver.find_elements_by_css_selector("#calc_resource > option")
+        resources = self.driver.find_elements(
+            By.CSS_SELECTOR, "#calc_resource > option"
+        )
         self.assertEqual(len(resources), 2)
         self.assertEqual(resources[0].text, "Local")
         self.assertFalse(resources[0].is_selected())
@@ -277,7 +283,9 @@ def test_autoselect_resource_remote(self):
         self.launch_ensemble_next_step()
         self.wait_for_ajax()
 
-        resources = self.driver.find_elements_by_css_selector("#calc_resource > option")
+        resources = self.driver.find_elements(
+            By.CSS_SELECTOR, "#calc_resource > option"
+        )
         self.assertEqual(len(resources), 2)
         self.assertEqual(resources[0].text, "Local")
         self.assertFalse(resources[0].is_selected())
@@ -303,7 +311,9 @@ def test_autoselect_resource_local(self):
 
         self.lget("/launch/")
 
-        resources = self.driver.find_elements_by_css_selector("#calc_resource > option")
+        resources = self.driver.find_elements(
+            By.CSS_SELECTOR, "#calc_resource > option"
+        )
         self.assertEqual(len(resources), 2)
         self.assertEqual(resources[0].text, "Local")
         self.assertTrue(resources[0].is_selected())
@@ -313,7 +323,9 @@ def test_autoselect_resource_local(self):
 
         self.calc_input_params(params)
 
-        resources = self.driver.find_elements_by_css_selector("#calc_resource > option")
+        resources = self.driver.find_elements(
+            By.CSS_SELECTOR, "#calc_resource > option"
+        )
         self.assertEqual(len(resources), 2)
         self.assertEqual(resources[0].text, "Local")
         self.assertTrue(resources[0].is_selected())
@@ -330,7 +342,9 @@ def test_autoselect_resource_local(self):
         self.launch_ensemble_next_step()
         self.wait_for_ajax()
 
-        resources = self.driver.find_elements_by_css_selector("#calc_resource > option")
+        resources = self.driver.find_elements(
+            By.CSS_SELECTOR, "#calc_resource > option"
+        )
         self.assertEqual(len(resources), 2)
         self.assertEqual(resources[0].text, "Local")
         self.assertTrue(resources[0].is_selected())

diff --git a/frontend/test_selenium.py b/frontend/test_selenium.py
@@ -853,12 +853,12 @@ def test_load_preset(self):
 
         self.load_preset("Test Preset")
 
-        solvent = self.driver.find_element_by_name("calc_solvent")
-        theory = Select(self.driver.find_element_by_id("calc_theory_level"))
-        func = self.driver.find_element_by_id("calc_functional")
-        basis_set = self.driver.find_element_by_id("calc_basis_set")
-        specifications = self.driver.find_element_by_id("calc_specifications")
-        software = self.driver.find_element_by_id("calc_software")
+        solvent = self.driver.find_element(By.NAME, "calc_solvent")
+        theory = Select(self.driver.find_element(By.ID, "calc_theory_level"))
+        func = self.driver.find_element(By.ID, "calc_functional")
+        basis_set = self.driver.find_element(By.ID, "calc_basis_set")
+        specifications = self.driver.find_element(By.ID, "calc_specifications")
+        software = self.driver.find_element(By.ID, "calc_software")
 
         self.assertEqual(solvent.get_attribute("value"), params["solvent"])
         self.assertEqual(theory.first_selected_option.text, params["theory"])
@@ -893,18 +893,18 @@ def test_project_preset(self):
         self.click_project("My Project")
         self.create_molecule_in_project()
 
-        solvent = self.driver.find_element_by_name("calc_solvent")
+        solvent = self.driver.find_element(By.NAME, "calc_solvent")
         solvation_model = Select(
-            self.driver.find_element_by_name("calc_solvation_model")
+            self.driver.find_element(By.NAME, "calc_solvation_model")
         )
         solvation_radii = Select(
-            self.driver.find_element_by_name("calc_solvation_radii")
+            self.driver.find_element(By.NAME, "calc_solvation_radii")
         )
-        theory = Select(self.driver.find_element_by_id("calc_theory_level"))
-        func = self.driver.find_element_by_id("calc_functional")
-        basis_set = self.driver.find_element_by_id("calc_basis_set")
-        software = self.driver.find_element_by_id("calc_software")
-        specifications = self.driver.find_element_by_id("calc_specifications")
+        theory = Select(self.driver.find_element(By.ID, "calc_theory_level"))
+        func = self.driver.find_element(By.ID, "calc_functional")
+        basis_set = self.driver.find_element(By.ID, "calc_basis_set")
+        software = self.driver.find_element(By.ID, "calc_software")
+        specifications = self.driver.find_element(By.ID, "calc_specifications")
 
         self.assertEqual(solvent.get_attribute("value"), params["solvent"])
         self.assertEqual(
@@ -1549,7 +1549,7 @@ def test_request_PI(self):
         self.lget("/profile/")
         self.apply_PI("Test group")
         self.assertTrue(
-            self.driver.find_element_by_id("PI_application_message").text.find(
+            self.driver.find_element(By.ID, "PI_application_message").text.find(
                 "Your request has been received"
             )
             != -1
@@ -1993,7 +1993,7 @@ def test_ensemble_second_step(self):
         }
         self.calc_input_params(params2)
 
-        charge = self.driver.find_element_by_name("calc_charge")
+        charge = self.driver.find_element(By.NAME, "calc_charge")
         self.assertEqual(charge.get_attribute("value"), params["charge"])
 
         self.calc_launch()
@@ -2027,7 +2027,7 @@ def test_ensemble_second_step_mult(self):
         }
         self.calc_input_params(params2)
 
-        mult = self.driver.find_element_by_name("calc_multiplicity")
+        mult = self.driver.find_element(By.NAME, "calc_multiplicity")
         self.assertEqual(mult.get_attribute("value"), params["multiplicity"])
 
     def test_structure_second_step(self):
@@ -2054,7 +2054,7 @@ def test_structure_second_step(self):
             # project and charge implicit
         }
 
-        charge = self.driver.find_element_by_name("calc_charge")
+        charge = self.driver.find_element(By.NAME, "calc_charge")
         self.assertEqual(charge.get_attribute("value"), params["charge"])
 
         self.calc_input_params(params2)
@@ -2277,12 +2277,12 @@ def test_default_settings_from_ensemble(self):
 
         self.launch_ensemble_next_step()
 
-        solvent = self.driver.find_element_by_name("calc_solvent")
-        charge = self.driver.find_element_by_name("calc_charge")
+        solvent = self.driver.find_element(By.NAME, "calc_solvent")
+        charge = self.driver.find_element(By.NAME, "calc_charge")
         solvation_model = Select(
-            self.driver.find_element_by_name("calc_solvation_model")
+            self.driver.find_element(By.NAME, "calc_solvation_model")
         )
-        software = self.driver.find_element_by_id("calc_software")
+        software = self.driver.find_element(By.ID, "calc_software")
 
         self.assertEqual(solvent.get_attribute("value"), params["solvent"])
         self.assertEqual(charge.get_attribute("value"), params["charge"])
@@ -2314,12 +2314,12 @@ def test_default_settings_from_structure(self):
 
         self.launch_structure_next_step()
 
-        solvent = self.driver.find_element_by_name("calc_solvent")
-        charge = self.driver.find_element_by_name("calc_charge")
+        solvent = self.driver.find_element(By.NAME, "calc_solvent")
+        charge = self.driver.find_element(By.NAME, "calc_charge")
         solvation_model = Select(
-            self.driver.find_element_by_name("calc_solvation_model")
+            self.driver.find_element(By.NAME, "calc_solvation_model")
         )
-        software = self.driver.find_element_by_id("calc_software")
+        software = self.driver.find_element(By.ID, "calc_software")
 
         self.assertEqual(solvent.get_attribute("value"), params["solvent"])
         self.assertEqual(charge.get_attribute("value"), params["charge"])
@@ -2351,12 +2351,12 @@ def test_default_settings_from_frame(self):
         self.details_first_calc()
         self.launch_frame_next_step()
 
-        solvent = self.driver.find_element_by_name("calc_solvent")
-        charge = self.driver.find_element_by_name("calc_charge")
+        solvent = self.driver.find_element(By.NAME, "calc_solvent")
+        charge = self.driver.find_element(By.NAME, "calc_charge")
         solvation_model = Select(
-            self.driver.find_element_by_name("calc_solvation_model")
+            self.driver.find_element(By.NAME, "calc_solvation_model")
         )
-        software = self.driver.find_element_by_id("calc_software")
+        software = self.driver.find_element(By.ID, "calc_software")
 
         self.assertEqual(solvent.get_attribute("value"), params["solvent"])
         self.assertEqual(charge.get_attribute("value"), params["charge"])
@@ -4058,7 +4058,7 @@ def test_input_file_present(self):
         self.details_latest_order()
         self.details_first_calc()
 
-        input_file = self.driver.find_element_by_css_selector(".textarea")
+        input_file = self.driver.find_element(By.CSS_SELECTOR, ".textarea")
         assert len(input_file.text) > 10
 
     def test_sp_from_frame(self):

diff --git a/frontend/tests/cache/frontend.test_calculations.OrcaCalculationTests.test_ts_DFT.input b/frontend/tests/cache/frontend.test_calculations.OrcaCalculationTests.test_ts_DFT.input
@@ -6,6 +6,9 @@ H    1.99826837   0.05502843   0.00651241
 H    0.59453997  -0.48560162   0.83949232
 H    0.66998094  -0.58930117  -0.87511947
 *
+%geom
+Calc_Hess true
+end
 %pal
 nprocs 4
 end
diff --git a/frontend/tests/cache/frontend.test_calculations.OrcaCalculationTests.test_ts_DFT/calc.inp b/frontend/tests/cache/frontend.test_calculations.OrcaCalculationTests.test_ts_DFT/calc.inp
@@ -5,6 +5,9 @@ H    1.99826837   0.05502843   0.00651241
 H    0.59453997  -0.48560162   0.83949232
 H    0.66998094  -0.58930117  -0.87511947
 *
+%geom
+Calc_Hess true
+end
 %pal
 nprocs 4
 end