Merge branch 'dev' into deploy

biosimulators_test_suite/_version.py

@@ -1 +1 @@
-__version__ = '0.1.83'
+__version__ = '0.1.84'

biosimulators_test_suite/config.py

@@ -20,7 +20,8 @@ class Config(object):
         biosimulators_audience (:obj:`str`): Open API audience for the BioSimulators API
         biosimulators_api_client_id (:obj:`str`): Client id of the BioSimulators API
         biosimulators_api_client_secret (:obj:`str`): Client secret of the BioSimulators API
-        biosimulators_api_endpoint (:obj:`str`): Base URL for the BioSimulators API
+        biosimulators_prod_api_endpoint (:obj:`str`): Base URL for the BioSimulators API
+        biosimulators_dev_api_endpoint (:obj:`str`): Base URL for the BioSimulators API
         biosimulators_curator_gh_ids (:obj:`list` of :obj:`str`): GitHub user ids of the BioSimulators curators
         biosimulators_default_specifications_version (:obj:`str`): Default version of the BioSimulators simulation specifications
         biosimulators_default_image_version (:obj:`str`): Default version of the BioSimulators Docker image format
@@ -47,7 +48,8 @@ def __init__(self,
                  pull_docker_image=None, docker_hub_username=None, docker_hub_token=None,
                  biosimulators_auth_endpoint=None, biosimulators_audience=None,
                  biosimulators_api_client_id=None, biosimulators_api_client_secret=None,
-                 biosimulators_api_endpoint=None,
+                 biosimulators_prod_api_endpoint=None,
+                 biosimulators_dev_api_endpoint=None,
                  biosimulators_curator_gh_ids=None, biosimulators_default_specifications_version=None,
                  biosimulators_default_image_version=None, biosimulators_docker_registry_url=None,
                  biosimulators_docker_registry_username=None, biosimulators_docker_registry_token=None,
@@ -67,7 +69,8 @@ def __init__(self,
             biosimulators_audience (:obj:`str`, optional): Open API audience for the BioSimulators API
             biosimulators_api_client_id (:obj:`str`, optional): Client id of the BioSimulators API
             biosimulators_api_client_secret (:obj:`str`, optional): Client secret of the BioSimulators API
-            biosimulators_api_endpoint (:obj:`str`, optional): Base URL for the BioSimulators API
+            biosimulators_prod_api_endpoint (:obj:`str`, optional): Base URL for the BioSimulators API
+            biosimulators_dev_api_endpoint (:obj:`str`, optional): Base URL for the BioSimulators API
             biosimulators_curator_gh_ids (:obj:`list` of :obj:`str`, optional): GitHub user ids of the BioSimulators curators
             biosimulators_default_specifications_version (:obj:`str`, optional): Default version of the BioSimulators simulation specifications
             biosimulators_default_image_version (:obj:`str`, optional): Default version of the BioSimulators Docker image format
@@ -127,10 +130,15 @@ def __init__(self,
         else:
             self.biosimulators_api_client_secret = biosimulators_api_client_secret
 
-        if biosimulators_api_endpoint is None:
-            self.biosimulators_api_endpoint = os.getenv('BIOSIMULATORS_API_ENDPOINT', 'https://api.biosimulators.org/')
+        if biosimulators_prod_api_endpoint is None:
+            self.biosimulators_prod_api_endpoint = os.getenv('BIOSIMULATORS_PROD_API_ENDPOINT', 'https://api.biosimulators.org/')
         else:
-            self.biosimulators_api_endpoint = biosimulators_api_endpoint
+            self.biosimulators_prod_api_endpoint = biosimulators_prod_api_endpoint
+
+        if biosimulators_dev_api_endpoint is None:
+            self.biosimulators_dev_api_endpoint = os.getenv('BIOSIMULATORS_DEV_API_ENDPOINT', 'https://api.biosimulators.dev/')
+        else:
+            self.biosimulators_dev_api_endpoint = biosimulators_dev_api_endpoint
 
         if biosimulators_curator_gh_ids is None:
             ids = os.getenv('BIOSIMULATORS_CURATOR_GH_IDS', 'jonrkarr').strip()

biosimulators_test_suite/exec_gh_action.py

@@ -14,7 +14,7 @@
 from .results.io import write_test_results
 from .utils import get_singularity_image_filename
 from biosimulators_utils.biosimulations.utils import validate_biosimulations_api_response
-from biosimulators_utils.config import Colors
+from biosimulators_utils.config import Colors, Config as BioSimulatorsUtilsConfig
 from biosimulators_utils.gh_action.data_model import Comment, GitHubActionCaughtError  # noqa: F401
 from biosimulators_utils.gh_action.core import GitHubAction, GitHubActionErrorHandling
 from biosimulators_utils.image import get_docker_image
@@ -96,7 +96,8 @@ def run(self):
         self.add_labels_to_issue(self.issue_number, [IssueLabel.validated.value])
 
         # get specifications of other versions of simulator
-        existing_version_specifications = get_simulator_version_specs(specifications['id'])
+        config = BioSimulatorsUtilsConfig()
+        existing_version_specifications = get_simulator_version_specs(specifications['id'], config)
 
         # determine if simulator is approved: issue is a revision of an existing version of a validated simulator,
         # a new version of a validated simulator, or the issue has been manually approved by the BioSimulators Team
@@ -445,7 +446,12 @@ def commit_simulator(self, submission, specifications, existing_version_specific
             specifications['biosimulators']['validated'] = False
             specifications['biosimulators']['validationTests'] = None
 
-        self.post_entry_to_biosimulators_api(specifications, existing_version_specifications)
+        config = BioSimulatorsUtilsConfig(BIOSIMULATORS_API_ENDPOINT=self.config.biosimulators_prod_api_endpoint)
+        self.post_entry_to_biosimulators_api(specifications, existing_version_specifications, self.config.biosimulators_prod_api_endpoint)
+
+        config = BioSimulatorsUtilsConfig(BIOSIMULATORS_API_ENDPOINT=self.config.biosimulators_dev_api_endpoint)
+        existing_version_specifications = get_simulator_version_specs(specifications['id'], config)
+        self.post_entry_to_biosimulators_api(specifications, existing_version_specifications, self.config.biosimulators_dev_api_endpoint)
 
         # commit image
         if submission.validate_image:
@@ -528,12 +534,13 @@ def trigger_conversion_of_docker_image_to_singularity(self, specifications):
                                  })
         validate_biosimulations_api_response(response, 'A Singularity image could not be generated for the Docker image')
 
-    def post_entry_to_biosimulators_api(self, specifications, existing_version_specifications):
+    def post_entry_to_biosimulators_api(self, specifications, existing_version_specifications, biosimulators_api_endpoint):
         """ 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
+            biosimulators_api_endpoint (:obj:`str`): endpoint for the BioSimulators API (e.g., ``https://api.biosimulators.org``)
         """
         auth_headers = self.get_auth_headers_for_biosimulations_api(
             self.config.biosimulators_auth_endpoint, self.config.biosimulators_audience,
@@ -542,11 +549,11 @@ def post_entry_to_biosimulators_api(self, specifications, existing_version_speci
         existing_versions = [existing_version_spec['version'] for existing_version_spec in existing_version_specifications]
         update_simulator = specifications['version'] in existing_versions
         if update_simulator:
-            endpoint = '{}simulators/{}/{}'.format(self.config.biosimulators_api_endpoint, specifications['id'], specifications['version'])
+            endpoint = '{}simulators/{}/{}'.format(biosimulators_api_endpoint, specifications['id'], specifications['version'])
             requests_method = requests.put
             method = 'updated'
         else:
-            endpoint = '{}simulators'.format(self.config.biosimulators_api_endpoint)
+            endpoint = '{}simulators'.format(biosimulators_api_endpoint)
             requests_method = requests.post
             method = 'added'
         response = requests_method(endpoint, headers=auth_headers, json=specifications)

biosimulators_test_suite/test_case/published_project.py

@@ -320,9 +320,6 @@ def eval(self, specifications, working_dirname, synthetic_archives_dir=None, dry
         if dry_run:
             return
 
-        if not os.path.isdir(working_dirname):
-            os.makedirs(working_dirname)
-
         # pull image and execute COMBINE/OMEX archive for case
         try:
             self.exec_sedml_docs_in_archive(specifications, working_dirname, cli=cli)

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn] >= 0.1.144
+biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn] >= 0.1.160
 cement
 docker
 natsort

tests/test_case/test_published_project.py

@@ -218,6 +218,9 @@ def exec_archive(error, missing_report, extra_report, missing_data_set, extra_da
                 data[0][0] = -1
                 data[1][0] = -1
 
+            if not os.path.isdir(out_dir):
+                os.makedirs(out_dir)
+
             if extra_report:
                 report = Report(id='report', data_sets=[DataSet(id=i, label=l) for i, l in zip(ids, labels)])
                 data_set_results = DataSetResults({i: d for i, d in zip(ids, data)})
@@ -229,6 +232,7 @@ def exec_archive(error, missing_report, extra_report, missing_data_set, extra_da
                 ReportWriter().run(report, data_set_results, out_dir, 'BIOMD0000000912_sim.sedml/report', ReportFormat.h5)
 
             plot_file = os.path.join(out_dir, 'plot.pdf')
+
             with open(plot_file, 'w'):
                 pass
 

tests/test_config.py

@@ -43,7 +43,8 @@ def test_arguments(self):
             pull_docker_image=True, docker_hub_username='user', docker_hub_token='token',
             biosimulators_auth_endpoint='https://auth.biosimulators.org', biosimulators_audience='biosimulators_audience',
             biosimulators_api_client_id='biosimulators_client_id', biosimulators_api_client_secret='biosimulators_client_secret',
-            biosimulators_api_endpoint='https://api.biosimulators.org',
+            biosimulators_prod_api_endpoint='https://api.biosimulators.org',
+            biosimulators_dev_api_endpoint='https://api.biosimulators.dev',
             biosimulators_curator_gh_ids=['user'], biosimulators_default_specifications_version='1.0.0',
             biosimulators_default_image_version='1.0.0', biosimulators_docker_registry_url='ghcr.io',
             biosimulators_docker_registry_username='[email protected]', biosimulators_docker_registry_token='[email protected]',
@@ -60,7 +61,8 @@ def test_arguments(self):
         self.assertEqual(config.biosimulators_audience, 'biosimulators_audience')
         self.assertEqual(config.biosimulators_api_client_id, 'biosimulators_client_id')
         self.assertEqual(config.biosimulators_api_client_secret, 'biosimulators_client_secret')
-        self.assertEqual(config.biosimulators_api_endpoint, 'https://api.biosimulators.org')
+        self.assertEqual(config.biosimulators_prod_api_endpoint, 'https://api.biosimulators.org')
+        self.assertEqual(config.biosimulators_dev_api_endpoint, 'https://api.biosimulators.dev')
         self.assertEqual(config.biosimulators_curator_gh_ids, ['user'])
         self.assertEqual(config.biosimulators_default_specifications_version, '1.0.0')
         self.assertEqual(config.biosimulators_default_image_version, '1.0.0')

tests/test_exec_gh_action.py

@@ -318,14 +318,14 @@ def post(self, url, json=None, headers=None):
                     self.parent.assertIn('grant_type', json)
                     return mock.Mock(raise_for_status=lambda: None, json=lambda: {'token_type': 'Bearer', 'access_token': '******'})
                 else:
-                    self.parent.assertEqual(url, Config().biosimulators_api_endpoint + 'simulators')
+                    self.parent.assertEqual(url, Config().biosimulators_prod_api_endpoint + 'simulators')
                     self.parent.assertEqual(headers, {'Authorization': 'Bearer ******'})
                     self.parent.assertEqual(json, {'id': 'tellurium', 'version': '2.1.6'})
                     return mock.Mock(raise_for_status=lambda: None)
 
             def put(self, url, json=None, headers=None):
                 self.n_put = self.n_put + 1
-                self.parent.assertEqual(url, Config().biosimulators_api_endpoint + 'simulators/tellurium/2.1.6')
+                self.parent.assertEqual(url, Config().biosimulators_prod_api_endpoint + 'simulators/tellurium/2.1.6')
                 self.parent.assertEqual(json, {'id': 'tellurium', 'version': '2.1.6'})
                 return mock.Mock(raise_for_status=lambda: None)
 
@@ -335,14 +335,14 @@ def put(self, url, json=None, headers=None):
         existing_version_specs = [{'id': 'tellurium', 'version': '2.1.6'}]
         with mock.patch('requests.post', side_effect=requests_mock.post):
             with mock.patch('requests.put', side_effect=requests_mock.put):
-                action.post_entry_to_biosimulators_api(specs, existing_version_specs)
+                action.post_entry_to_biosimulators_api(specs, existing_version_specs, action.config.biosimulators_prod_api_endpoint)
         self.assertEqual(requests_mock.n_post, 1)
         self.assertEqual(requests_mock.n_put, 1)
 
         existing_version_specs = [{'id': 'tellurium', 'version': '2.1.5'}]
         with mock.patch('requests.post', side_effect=requests_mock.post):
             with mock.patch('requests.put', side_effect=requests_mock.put):
-                action.post_entry_to_biosimulators_api(specs, existing_version_specs)
+                action.post_entry_to_biosimulators_api(specs, existing_version_specs, action.config.biosimulators_prod_api_endpoint)
         self.assertEqual(requests_mock.n_post, 3)
         self.assertEqual(requests_mock.n_put, 1)
 
@@ -368,22 +368,22 @@ def put(self, url, json=None, headers=None, auth=None):
         existing_version_specs = [{'id': 'tellurium', 'version': '2.1.5'}]
         with mock.patch('requests.post', side_effect=requests_mock.post):
             action.commit_simulator(SimulatorSubmission(validate_image=False), specs, existing_version_specs, [])
-        self.assertEqual(requests_mock.n_post, 2)
+        self.assertEqual(requests_mock.n_post, 2 + 2)
 
         existing_version_specs = [{'id': 'tellurium', 'version': '2.1.5'}]
         with mock.patch.dict(os.environ, self.env):
             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, 6)
+        self.assertEqual(requests_mock.n_post, 6 + 4)
 
         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, 7)
-        self.assertEqual(requests_mock.n_put, 1)
+        self.assertEqual(requests_mock.n_post, 7 + 6)
+        self.assertEqual(requests_mock.n_put, 1 + 0)
 
     def test_run(self):
         # validate specs of valid new simulator, fail on invalid specs
@@ -716,7 +716,10 @@ def get(self, url, json=None, auth=None, headers=None):
                     }
                 elif url == 'https://api.github.com/repos/biosimulators/Biosimulators/issues/11/labels':
                     response = [{'name': label} for label in self.issue_labels]
-                elif url == Config().biosimulators_api_endpoint + 'simulators/tellurium':
+                elif url in [
+                    Config().biosimulators_prod_api_endpoint + 'simulators/tellurium',
+                    Config().biosimulators_dev_api_endpoint + 'simulators/tellurium',
+                ]:
                     response = self.simulator_versions
                 else:
                     raise ValueError('Invalid url: {}'.format(url))
@@ -726,11 +729,17 @@ def post(self, url, json=None, auth=None, headers=None):
                 if url == Config().biosimulators_auth_endpoint:
                     error = None
                     response = {'token_type': 'Bearer', 'access_token': '******'}
-                elif url == Config().biosimulators_api_endpoint + 'simulators':
+                elif url in [
+                    Config().biosimulators_prod_api_endpoint + 'simulators',
+                    Config().biosimulators_dev_api_endpoint + 'simulators',
+                ]:
                     self.simulator_versions.append(json)
                     error = None
                     response = None
-                elif url == Config().biosimulators_api_endpoint + 'simulators/validate':
+                elif url in [
+                    Config().biosimulators_prod_api_endpoint + 'simulators/validate',
+                    Config().biosimulators_dev_api_endpoint + 'simulators/validate',
+                ]:
                     if self.specs_valid:
                         error = None
                         response = None
@@ -775,7 +784,10 @@ def patch(self, url, json=None, auth=None, headers=None):
                 return mock.Mock(raise_for_status=lambda: None, json=lambda: response)
 
             def put(self, url, json=None, auth=None, headers=None):
-                if url.startswith(Config().biosimulators_api_endpoint + 'simulators/tellurium/'):
+                if (
+                    url.startswith(Config().biosimulators_prod_api_endpoint + 'simulators/tellurium/') or
+                    url.startswith(Config().biosimulators_dev_api_endpoint + 'simulators/tellurium/')
+                ):
                     for i_version, version in enumerate(self.simulator_versions):
                         if version['version'] == json['version']:
                             self.simulator_versions[i_version] = json