Merge branch 'dev' into deploy

biosimulators · Dec 28, 2020 · 70ec4c5 · 70ec4c5
2 parents f91ccc2 + dcf53b0
commit 70ec4c5
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Showing 5 changed files with 32 additions and 9 deletions.
diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
@@ -1 +1 @@
-__version__ = '0.1.4'
+__version__ = '0.1.5'
diff --git a/biosimulators_test_suite/exec_core.py b/biosimulators_test_suite/exec_core.py
@@ -184,7 +184,7 @@ def run(self):
                 print(termcolor.colored(result.type.value, TERMINAL_COLORS[result.type.value]), end='')
                 print(' (', end='')
                 if result.warnings:
-                    print(termcolor.colored(str(len(result.warnings)) + ', ', TERMINAL_COLORS['warned']), end='')
+                    print(termcolor.colored(str(len(result.warnings)) + ' warnings, ', TERMINAL_COLORS['warned']), end='')
                 print('{:.1f} s'.format(result.duration), end='')
                 print(').')
 

diff --git a/biosimulators_test_suite/test_case/published_project.py b/biosimulators_test_suite/test_case/published_project.py
@@ -165,6 +165,7 @@ def from_dict(self, data):
             id = exp_report_def['id']
 
             data_set_labels = set(exp_report_def.get('dataSets', []))
+            points = tuple(exp_report_def['points'])
 
             values = {}
             for key, val in exp_report_def.get('values', {}).items():
@@ -173,7 +174,20 @@ def from_dict(self, data):
                 else:
                     values[key] = {}
                     for k, v in val.items():
-                        values[key][tuple(int(index) for index in k.split(","))] = v
+                        multi_index = tuple(int(index) for index in k.split(","))
+                        try:
+                            numpy.ravel_multi_index([multi_index], points)[0]
+                        except ValueError:
+                            raise ValueError((
+                                "Key '{}' of the expected values of report '{}' of published project test case '{}' is invalid. "
+                                "Key must be less than or equal to '{}'."
+                            ).format(
+                                multi_index,
+                                self.id,
+                                self.id.replace('published_project.PublishedProjectTestCase:', ''),
+                                tuple(p - 1 for p in points),
+                            ))
+                        values[key][multi_index] = v
 
             invalid_dataset_ids = set(values.keys()).difference(set(data_set_labels))
             if invalid_dataset_ids:
@@ -187,7 +201,7 @@ def from_dict(self, data):
             self.expected_reports.append(ExpectedSedReport(
                 id=id,
                 data_sets=data_set_labels,
-                points=tuple(exp_report_def['points']),
+                points=points,
                 values=values,
             ))
 
@@ -305,16 +319,17 @@ def eval(self, specifications):
                         value = report.loc[data_set_label, :]
                         for el_id, expected_el_value in expected_value.items():
                             el_index = numpy.ravel_multi_index([el_id], value.shape)[0]
+                            actual_el_value = value[el_index]
                             try:
                                 numpy.testing.assert_allclose(
-                                    value[el_index],
+                                    actual_el_value,
                                     expected_el_value,
                                     rtol=self.r_tol,
                                     atol=self.a_tol,
                                 )
                             except AssertionError:
                                 errors.append('Data set {} of report {} does not have expected value at {}: {} != {}'.format(
-                                    data_set_label, expected_report.id, el_id, value[el_index], expected_el_value))
+                                    data_set_label, expected_report.id, el_id, actual_el_value, expected_el_value))
                     else:
                         try:
                             numpy.testing.assert_allclose(

diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.json b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.json
@@ -12,7 +12,7 @@
     "values": {
       "time": {
         "0": 0.0,
-        "301": 5100.0
+        "300": 5100.0
       }
     }
   }],

diff --git a/tests/test_case/test_published_project.py b/tests/test_case/test_published_project.py
@@ -74,11 +74,19 @@ def test_CuratedCombineArchiveTestCase_from_dict_error_handling(self):
         filename = os.path.join('sbml-core', 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.json')
         with open(os.path.join(base_path, filename), 'r') as file:
             data = json.load(file)
-        data['expectedReports'][0]['values']['t'] = [0, 1, 2, 3, 4, 5]
+        id = 'published_project.PublishedProjectTestCase:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.json'
+
+        data['expectedReports'][0]['values'] = {'t': [0, 1, 2, 3, 4, 5]}
         with self.assertRaisesRegex(ValueError, "keys were not in the 'dataSets' property"):
-            id = 'published_project.PublishedProjectTestCase:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.json'
             PublishedProjectTestCase(id=id).from_dict(data)
 
+        data['expectedReports'][0]['values'] = {'T': {'5001': 1000.2}}
+        with self.assertRaisesRegex(ValueError, "Key must be less than or equal to"):
+            PublishedProjectTestCase(id=id).from_dict(data)
+
+        data['expectedReports'][0]['values'] = {'T': {'5000': 1000.}}
+        PublishedProjectTestCase(id=id).from_dict(data)
+
     def test_CuratedCombineArchiveTestCase_from_json(self):
         base_path = os.path.join(os.path.dirname(__file__), '..', '..', 'examples')
         filename = os.path.join('sbml-core', 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.json')