Bug fixes and update to tests

Author: RaphaelRobidas

frontend/calculation_unittest.py

@@ -47,6 +47,10 @@ def setUp(self):
         self.profile.is_PI = True
         self.profile.save()
 
+        self.name_patcher = mock.patch.dict(os.environ, {"TEST_NAME": self.id()})
+        self.name_patcher.start()
+
+
     def get_params(self, **modifications):
         params = self.params.copy()
 

frontend/calcusliveserver.py

@@ -22,11 +22,11 @@
 import time
 import sys
 import glob
-from django.contrib.staticfiles.testing import StaticLiveServerTestCase
 import selenium
 import datetime
 import pexpect
 import socket
+from unittest import mock
 
 from selenium import webdriver
 from selenium.webdriver.common.alert import Alert
@@ -43,6 +43,7 @@
 from celery.contrib.testing.worker import start_worker
 from celery.contrib.abortable import AbortableAsyncResult
 
+from django.contrib.staticfiles.testing import StaticLiveServerTestCase
 from django.core.management import call_command
 from django.contrib.auth.models import User, Group
 from .models import *
@@ -115,6 +116,7 @@ def tearDownClass(cls):
         super().tearDownClass()
 
     def run(self, result=None):
+        self.full_test_name = self.id()
         self.m_name = self._testMethodName
         self._testMethodName = "_test_wrapper"
         super(StaticLiveServerTestCase, self).run(result)
@@ -157,6 +159,10 @@ def setUp(self):
         self.profile = Profile.objects.get(user__username=self.username)
         time.sleep(0.1)#Reduces glitches (I think?)
 
+        self.name_patcher = mock.patch.dict(os.environ, {"TEST_NAME": self.full_test_name})
+        self.name_patcher.start()
+
+
     def cleanupCalculations(self):
         for c in Calculation.objects.all():
             res = AbortableAsyncResult(c.task_id)
@@ -1137,6 +1143,7 @@ def get_calculation_statuses(self):
 
     def apply_PI(self, group_name):
         assert self.is_on_page_profile()
+        self.wait_for_ajax()
         group_name = self.driver.find_element_by_name('group_name')
         submit = self.driver.find_element_by_css_selector("button.button:nth-child(3)")
         group_name.send_keys("Test group")
@@ -1163,6 +1170,7 @@ def accept_PI_request(self):
 
     def wait_latest_calc_done(self, timeout):
         assert self.is_on_page_calculations()
+        self.wait_for_ajax()
         assert self.get_number_calc_orders() > 0
 
         for i in range(0, timeout, 2):
@@ -1580,6 +1588,7 @@ def get_name_presets(self):
         return names
 
     def select_preset(self, name):
+        self.wait_for_ajax()
         element = WebDriverWait(self.driver, 2).until(
             EC.presence_of_element_located((By.XPATH, "//*[@id='presets']/option[text()='{}']".format(name)))
         )

frontend/gen_calc.py

@@ -114,7 +114,7 @@ def gen_calc(params, profile):
 
     proj = Project.objects.create()
     dummy = CalculationOrder.objects.create(project=proj, author=profile)
-    calc = Calculation.objects.create(structure=s, step=step, parameters=p, order=dummy)
+    calc = Calculation.objects.create(structure=s, step=step, parameters=p, order=dummy, task_id=1)
 
     if step.creates_ensemble:
         calc.result_ensemble = Ensemble.objects.create(parent_molecule=mol)
@@ -123,8 +123,9 @@ def gen_calc(params, profile):
         calc.constraints = params['constraints']
 
     if 'aux_file' in params:
-        aux_xyz = parse_xyz_from_file(os.path.join(TESTS_DIR, params['aux_file']))
-        aux_s = Structure.objects.create(parent_ensemble=e, number=2)
+        with open(os.path.join(TESTS_DIR, params['aux_file'])) as f:
+            aux_xyz = ''.join(f.readlines())
+        aux_s = Structure.objects.create(parent_ensemble=e, number=2, xyz_structure=aux_xyz)
         calc.aux_structure = aux_s
 
     calc.save()

frontend/tasks.py

@@ -315,6 +315,7 @@ def system(command, log_file="", force_local=False, software="xtb", calc_id=-1):
                     return ErrorCodes.UNKNOWN_TERMINATION
 
             if calc_id != -1 and res.is_aborted() == True:
+                logger.info(f"Stopping calculation {calc_id}")
                 signal_to_send = signal.SIGTERM
 
                 parent = psutil.Process(t.pid)
@@ -349,7 +350,7 @@ def get_cache_index(calc, cache_path):
     inputs = glob.glob(cache_path + '/*.input')
     for f in inputs:
         if files_are_equal(f, calc.input_file):
-            ind = f.split('/')[-1].split('.')[0]
+            ind = '.'.join(f.split('/')[-1].split('.')[:-1])
             return ind
     else:
         return -1
@@ -1031,6 +1032,7 @@ def orca_opt(in_file, calc):
         calc.structure = s
         calc.step = BasicStep.objects.get(name="Single-Point Energy")
         calc.save()
+        add_input_to_calc(calc)
         return orca_sp(in_file, calc)
 
     local_folder = os.path.join(CALCUS_SCR_HOME, str(calc.id))
@@ -1168,9 +1170,10 @@ def orca_freq(in_file, calc):
 
     with open(os.path.join(CALCUS_RESULTS_HOME, str(calc.id), "IR.csv"), 'w') as out:
         out.write("Wavenumber,Intensity\n")
-        intensities = 1000*np.array(intensities)/max(intensities)
-        for _x, i in sorted((zip(list(x), spectrum)), reverse=True):
-            out.write("-{:.1f},{:.5f}\n".format(_x, i))
+        if len(intensities) > 0:
+            intensities = 1000*np.array(intensities)/max(intensities)
+            for _x, i in sorted((zip(list(x), spectrum)), reverse=True):
+                out.write("-{:.1f},{:.5f}\n".format(_x, i))
 
     prop = get_or_create(calc.parameters, calc.structure)
     prop.energy = E
@@ -1193,6 +1196,11 @@ def orca_freq(in_file, calc):
             a, x, y, z = line.strip().split()
             struct.append([a, float(x), float(y), float(z)])
 
+    parse_orca_charges(calc, calc.structure)
+
+    if num_atoms == 1:
+        return ErrorCodes.SUCCESS
+
     while lines[ind].find("VIBRATIONAL FREQUENCIES") == -1 and ind > 0:
         ind -= 1
 
@@ -1256,8 +1264,6 @@ def is_all_null(arr):
             for ind2, (a, x, y, z) in enumerate(struct):
                 out.write("{} {:.4f} {:.4f} {:.4f} {} {} {}\n".format(a, x, y, z, *vibs[ind][3*ind2:3*ind2+3]))
 
-    parse_orca_charges(calc, calc.structure)
-
     return ErrorCodes.SUCCESS
 
 def orca_scan(in_file, calc):
@@ -1663,8 +1669,7 @@ def parse_default_orca_charges(calc, s):
 
 def parse_gaussian_charges(calc, s):
     parse_default_gaussian_charges(calc, s)
-
-    for spec in calc.parameters.specifications.split(' '):#The specifications have been cleaned/formatted already
+    for spec in calc.parameters.specifications.replace(', ', ',').split(' '):#The specifications have been cleaned/formatted already
         if spec.strip() == '':
             continue
         if spec.find('(') != -1:
@@ -2796,6 +2801,24 @@ def dispatcher(drawing, order_id):
         c.task_id = res
         c.save()
 
+def add_input_to_calc(calc):
+    inp = calc_to_ccinput(calc)
+    if isinstance(inp, CCInputException):
+        msg = f"CCInput error: {str(inp)}"
+        if is_test:
+            print(msg)
+        calc.error_message = msg
+        calc.status = 3
+        calc.save()
+        return ErrorCodes.FAILED_TO_CREATE_INPUT
+
+    calc.input_file = inp.input_file
+
+    calc.parameters.specifications = inp.confirmed_specifications
+
+    calc.save()
+    calc.parameters.save()
+
 @app.task(base=AbortableTask)
 def run_calc(calc_id):
     if not is_test:
@@ -2829,25 +2852,6 @@ def get_calc(calc_id):
         logger.info(f"Calc {calc_id} already revoked")
         return ErrorCodes.JOB_CANCELLED
 
-    def add_input_to_calc(calc):
-        inp = calc_to_ccinput(calc)
-        if isinstance(inp, CCInputException):
-            msg = f"CCInput error: {str(inp)}"
-            if is_test:
-                print(msg)
-            calc.error_message = msg
-            calc.status = 3
-            calc.save()
-            return ErrorCodes.FAILED_TO_CREATE_INPUT
-
-        calc.input_file = inp.input_file
-
-        if inp.confirmed_specifications != '':
-            calc.parameters.specifications = inp.confirmed_specifications
-
-        calc.save()
-        calc.parameters.save()
-
     if calc.parameters.software != "xtb": # xtb currently not directly supported by ccinput
         ret = add_input_to_calc(calc)
         if isinstance(ret, ErrorCodes):
@@ -2946,9 +2950,9 @@ def add_input_to_calc(calc):
         analyse_opt(calc.id)
 
     if is_test and os.getenv("CAN_USE_CACHED_LOGS") == "true" and os.getenv("USE_CACHED_LOGS") == "true" and not calc_is_cached(calc):
-        index = str(time()).replace('.', '_')
-        shutil.copytree(os.path.join(tests_dir, "scr", str(calc.id)), os.path.join(tests_dir, "cache", index))
-        with open(os.path.join(tests_dir, "cache", index+'.input'), 'w') as out:
+        test_name = os.environ['TEST_NAME']
+        shutil.copytree(os.path.join(tests_dir, "scr", str(calc.id)), os.path.join(tests_dir, "cache", test_name), dirs_exist_ok=True)
+        with open(os.path.join(tests_dir, "cache", test_name+'.input'), 'w') as out:
             out.write(calc.input_file)
 
     return ret

frontend/test_calculations.py

@@ -207,8 +207,7 @@ def test_freq_DFT(self):
 
     def test_freq_DFT_single_atom(self):
         self.assertTrue(self.run_test(type="Frequency Calculation", theory_level="DFT",
-                method="M062X", in_file="Cl.xyz", charge=-1,
-                callback=partial(self.cb_has_n_conformers, 1)))
+                method="M062X", in_file="Cl.xyz", charge=-1))
 
     def test_ts_SE(self):
         self.assertTrue(self.run_test(theory_level="Semi-empirical", method="AM1",

frontend/test_selenium.py

@@ -954,7 +954,7 @@ def test_duplicate_project_preset(self):
         param_count = Parameters.objects.count()
         self.assertEqual(param_count, 2)
 
-    def test_project_preset_independance(self):
+    def test_project_preset_independence(self):
         proj = Project.objects.create(name="My Project", author=self.profile)
         proj.save()