Merge branch 'dev' into deploy

biosimulators_test_suite/_version.py

@@ -1 +1 @@
-__version__ = '0.1.15'
+__version__ = '0.1.16'

biosimulators_test_suite/exec_gh_action.py

@@ -60,8 +60,18 @@ class ValidateCommitSimulatorGitHubAction(GitHubAction):
         issue_number (:obj:`str`): number of GitHub issue which triggered the action
     """
     BIOSIMULATORS_AUTH_ENDPOINT = 'https://auth.biosimulations.org/oauth/token'
-    BIOSIMULATORS_AUDIENCE = os.getenv('BIOSIMULATORS_AUDIENCE', 'api.biosimulators.org')
-    BIOSIMULATORS_API_ENDPOINT = os.getenv('BIOSIMULATORS_API_ENDPOINT', 'https://api.biosimulators.org/')
+    BIOSIMULATORS_AUDIENCE = os.getenv(
+        'BIOSIMULATORS_AUDIENCE',
+        'api.biosimulators.org')
+    RUNBIOSIMULATIONS_AUDIENCE = os.getenv(
+        'RUNBIOSIMULATIONS_AUDIENCE',
+        'dispatch.biosimulations.org')
+    BIOSIMULATORS_API_ENDPOINT = os.getenv(
+        'BIOSIMULATORS_API_ENDPOINT',
+        'https://api.biosimulators.org/')
+    RUNBIOSIMULATIONS_API_ENDPOINT = os.getenv(
+        'RUNBIOSIMULATIONS_API_ENDPOINT',
+        'https://run.api.biosimulations.dev/')
     DOCKER_REGISTRY_URL = 'ghcr.io'
     DOCKER_REGISTRY_IMAGE_URL_PATTERN = 'ghcr.io/biosimulators/{}:{}'
     DEFAULT_SPECIFICATIONS_VERSION = '1.0.0'
@@ -293,10 +303,14 @@ def commit_simulator(self, submission, specifications, existing_version_specific
             existing_version_specifications (:obj:`list` of :obj:`dict`): specifications of other versions of simulation tool
             test_results (:obj:`list` of :obj:`TestCaseResults`): results of test cases
         """
-        # copy image to BioSimulators namespace of Docker registry (GitHub Container Registry)
+        # commit image
         if submission.validate_image:
+            # copy image to BioSimulators namespace of Docker registry (GitHub Container Registry)
             self.push_image(specifications, existing_version_specifications)
 
+            # instruct runBioSimulations to generate a Singularity image for the Docker image
+            self.trigger_conversion_of_docker_image_to_singularity(specifications)
+
         # commit submission to BioSimulators database
         if 'biosimulators' not in specifications:
             specifications['biosimulators'] = {}
@@ -370,25 +384,30 @@ def is_submission_latest_version_of_simulator(self, specifications, existing_ver
                 return False
         return True
 
+    def trigger_conversion_of_docker_image_to_singularity(self, specifications):
+        """ Post the simulation to the BioSimulators database
+
+        Args:
+            specifications (:obj:`dict`): specifications of a simulation tool
+        """
+        auth_headers = self.get_auth_headers_for_biosimulations_api(self.RUNBIOSIMULATIONS_AUDIENCE)
+
+        response = requests.post(self.RUNBIOSIMULATIONS_API_ENDPOINT + 'images/refresh',
+                                 headers=auth_headers,
+                                 json={
+                                     'simulator': specifications['id'],
+                                     'version': specifications['version'],
+                                 })
+        response.raise_for_status()
+
     def post_entry_to_biosimulators_api(self, specifications, existing_version_specifications):
         """ Post the simulation to the BioSimulators database
 
         Args:
             specifications (:obj:`dict`): specifications of a simulation tool
             existing_version_specifications (:obj:`list` of :obj:`dict`): specifications of other versions of simulation tool
         """
-        api_id = os.getenv('BIOSIMULATORS_API_CLIENT_ID')
-        api_secret = os.getenv('BIOSIMULATORS_API_CLIENT_SECRET')
-
-        response = requests.post(self.BIOSIMULATORS_AUTH_ENDPOINT, json={
-            'client_id': api_id,
-            'client_secret': api_secret,
-            'audience': self.BIOSIMULATORS_AUDIENCE,
-            "grant_type": "client_credentials",
-        })
-        response.raise_for_status()
-        response_data = response.json()
-        auth_headers = {'Authorization': response_data['token_type'] + ' ' + response_data['access_token']}
+        auth_headers = self.get_auth_headers_for_biosimulations_api(self.BIOSIMULATORS_AUDIENCE)
 
         existing_versions = [existing_version_spec['version'] for existing_version_spec in existing_version_specifications]
         update_simulator = specifications['version'] in existing_versions
@@ -400,3 +419,26 @@ def post_entry_to_biosimulators_api(self, specifications, existing_version_speci
             requests_method = requests.post
         response = requests_method(endpoint, headers=auth_headers, json=specifications)
         response.raise_for_status()
+
+    def get_auth_headers_for_biosimulations_api(self, audience):
+        """ Get authorization headers for using one of the BioSimulations REST APIs
+        (BioSimulators, runBioSimulations, etc.).
+
+        Args:
+            audience (:obj:`str`): API audience
+
+        Returns:
+            :obj:`dict`: authorization headers
+        """
+        api_id = os.getenv('BIOSIMULATORS_API_CLIENT_ID')
+        api_secret = os.getenv('BIOSIMULATORS_API_CLIENT_SECRET')
+
+        response = requests.post(self.BIOSIMULATORS_AUTH_ENDPOINT, json={
+            'client_id': api_id,
+            'client_secret': api_secret,
+            'audience': audience,
+            "grant_type": "client_credentials",
+        })
+        response.raise_for_status()
+        response_data = response.json()
+        return {'Authorization': response_data['token_type'] + ' ' + response_data['access_token']}

tests/test_exec_gh_action.py

@@ -344,14 +344,14 @@ def put(self, url, json=None, headers=None, auth=None):
             with mock.patch('requests.post', side_effect=requests_mock.post):
                 with mock.patch.object(exec_gh_action.ValidateCommitSimulatorGitHubAction, 'push_image', return_value=None):
                     action.commit_simulator(SimulatorSubmission(validate_image=True), specs, existing_version_specs, [])
-        self.assertEqual(requests_mock.n_post, 4)
+        self.assertEqual(requests_mock.n_post, 6)
 
         existing_version_specs = [{'id': 'tellurium', 'version': '2.1.6'}]
         with mock.patch.dict(os.environ, self.env):
             with mock.patch('requests.post', side_effect=requests_mock.post):
                 with mock.patch('requests.put', side_effect=requests_mock.put):
                     action.commit_simulator(SimulatorSubmission(validate_image=False), specs, existing_version_specs, [])
-        self.assertEqual(requests_mock.n_post, 5)
+        self.assertEqual(requests_mock.n_post, 7)
         self.assertEqual(requests_mock.n_put, 1)
 
     def test_run(self):
@@ -365,6 +365,7 @@ def test_run(self):
             self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(requests_mock.simulator_versions, [])
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Invalid']))
         self.assertEqual(len(requests_mock.issue_messages), 2)
         self.assertRegex(requests_mock.issue_messages[-1], 'Specifications must be adhere to the BioSimulators schema')
@@ -381,6 +382,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(requests_mock.simulator_versions, [])
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated']))
         self.assertEqual(len(requests_mock.issue_messages), 2)
         self.assertEqual(requests_mock.issue_messages[-1], 'The specifications of your simulator is valid!')
@@ -398,6 +400,7 @@ def test_run(self):
             self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(requests_mock.simulator_versions, [])
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Invalid']))
         self.assertEqual(len(requests_mock.issue_messages), 3)
         self.assertRegex(requests_mock.issue_messages[-1], 'Singularity error')
@@ -415,6 +418,7 @@ def test_run(self):
             self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(requests_mock.simulator_versions, [])
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Invalid']))
         self.assertEqual(len(requests_mock.issue_messages), 4)
         self.assertRegex(requests_mock.issue_messages[-2], 'Passed 0 test cases')
@@ -432,6 +436,7 @@ def test_run(self):
             self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(requests_mock.simulator_versions, [])
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Invalid']))
         self.assertEqual(len(requests_mock.issue_messages), 4)
         self.assertRegex(requests_mock.issue_messages[-1], 'No test cases are applicable')
@@ -448,6 +453,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(requests_mock.simulator_versions, [])
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated']))
         self.assertEqual(len(requests_mock.issue_messages), 4)
         self.assertRegex(requests_mock.issue_messages[-2], 'Passed 1 test cases:')
@@ -465,6 +471,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'closed')
         self.assertEqual(set(v['version'] for v in requests_mock.simulator_versions), set(['2.1.6']))
+        self.assertEqual(requests_mock.refreshed_images, [{'simulator': 'tellurium', 'version': '2.1.6'}])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated', 'Approved']))
         self.assertEqual(len(requests_mock.issue_messages), 5)
         self.assertRegex(requests_mock.issue_messages[-1], 'Your submission was committed to the BioSimulators registry.')
@@ -489,6 +496,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(set(v['version'] for v in requests_mock.simulator_versions), set([]))
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated']))
         self.assertEqual(len(requests_mock.issue_messages), 5)
         self.assertRegex(requests_mock.issue_messages[-1], 'A member of the BioSimulators team will review your submission')
@@ -509,6 +517,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'open')
         self.assertEqual(set(v['version'] for v in requests_mock.simulator_versions), set(['2.1.5']))
+        self.assertEqual(requests_mock.refreshed_images, [])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated']))
         self.assertEqual(len(requests_mock.issue_messages), 5)
         self.assertRegex(requests_mock.issue_messages[-1], 'A member of the BioSimulators team will review your submission')
@@ -529,6 +538,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'closed')
         self.assertEqual(set(v['version'] for v in requests_mock.simulator_versions), set(['2.1.5', '2.1.6']))
+        self.assertEqual(requests_mock.refreshed_images, [{'simulator': 'tellurium', 'version': '2.1.6'}])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated', 'Approved']))
         self.assertEqual(len(requests_mock.issue_messages), 5)
         self.assertRegex(requests_mock.issue_messages[-1], 'Your submission was committed to the BioSimulators registry.')
@@ -554,6 +564,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'closed')
         self.assertEqual(set(v['version'] for v in requests_mock.simulator_versions), set(['2.1.5', '2.1.4']))
+        self.assertEqual(requests_mock.refreshed_images, [{'simulator': 'tellurium', 'version': '2.1.4'}])
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated', 'Approved']))
         self.assertEqual(len(requests_mock.issue_messages), 5)
         self.assertRegex(requests_mock.issue_messages[-1], 'Your submission was committed to the BioSimulators registry.')
@@ -577,6 +588,7 @@ def test_run(self):
         self._exec_run_mock_objs(requests_mock, docker_mock, validation_run_results)
         self.assertEqual(requests_mock.issue_state, 'closed')
         self.assertEqual(set(v['version'] for v in requests_mock.simulator_versions), set(['2.1.5']))
+        self.assertEqual(requests_mock.refreshed_images, [{'simulator': 'tellurium', 'version': '2.1.5'}])
         self.assertEqual(len(requests_mock.simulator_versions[-1]['biosimulators']['validationTests']['results']), 1)
         self.assertEqual(requests_mock.simulator_versions[-1]['biosimulators']['validationTests']['results'][0]['case']['id'], 'sedml.case-passed')
         self.assertEqual(requests_mock.issue_labels, set(['Validate/commit simulator', 'Validated', 'Approved']))
@@ -618,6 +630,8 @@ def __init__(self, submitted_version='2.1.6', new_simulator=True, previous_versi
                         },
                     ]
 
+                self.refreshed_images = []
+
                 self.issue_labels = set(['Validate/commit simulator'])
                 if previous_run_valid == True:
                     self.issue_labels.add('Validated')
@@ -687,6 +701,10 @@ def post(self, url, json=None, auth=None, headers=None):
                     else:
                         error = 'Specs are invalid'
                     response = None
+                elif url == exec_gh_action.ValidateCommitSimulatorGitHubAction.RUNBIOSIMULATIONS_API_ENDPOINT + 'images/refresh':
+                    self.refreshed_images.append(json)
+                    error = None
+                    response = None
                 elif url == 'https://api.github.com/repos/biosimulators/Biosimulators/issues/11/labels':
                     for label in json['labels']:
                         self.issue_labels.add(label)