minor improvements for validating simulators

biosimulators_utils/_version.py

@@ -1 +1 @@
-__version__ = '0.1.11'
+__version__ = '0.1.12'

biosimulators_utils/gh_action/core.py

@@ -29,29 +29,26 @@ class GitHubActionCaughtError(Exception):
 class GitHubActionErrorHandling(object):
     """ Methods for handing errors in the execution of GitHu actions """
     @classmethod
-    def catch_errors(cls, issue_number,
-                     uncaught_exception_msg_func=None,
+    def catch_errors(cls, uncaught_exception_msg_func=None,
                      caught_error_labels=None,
                      uncaught_error_labels=None):
         """ Generator for a decorator for CI actions that catches errors and reports them as comments to an issue
 
         Args:
-            issue_number (:obj:`str`): issue number
             uncaught_exception_msg_func (:obj:`types.FunctionType`, optional): function to calculate error message to display to users
             caught_error_labels (:obj:`list` of :obj:`str`, optional): labels to apply to caught errors
             uncaught_error_labels (:obj:`list` of :obj:`str`, optional): labels to apply to uncaught errors
         """
         if uncaught_exception_msg_func is None:
             uncaught_exception_msg_func = cls.get_uncaught_exception_msg
-        return functools.partial(cls._catch_errors, issue_number, uncaught_exception_msg_func,
+        return functools.partial(cls._catch_errors, uncaught_exception_msg_func,
                                  caught_error_labels or [], uncaught_error_labels or [])
 
     @staticmethod
-    def _catch_errors(issue_number, uncaught_exception_msg_func, caught_error_labels, uncaught_error_labels, func):
+    def _catch_errors(uncaught_exception_msg_func, caught_error_labels, uncaught_error_labels, func):
         """ Decorator for CI actions that catches errors and reports them as comments to an issue
 
         Args:
-            issue_number (:obj:`str`): issue number
             uncaught_exception_msg_func (:obj:`types.FunctionType`, optional): function to calculate error message to display to users
             caught_error_labels (:obj:`list` of :obj:`str`): labels to apply to caught errors
             uncaught_error_labels (:obj:`list` of :obj:`str`): labels to apply to uncaught errors
@@ -62,9 +59,11 @@ def wrapper(*args, **kwargs):
             try:
                 func(*args, **kwargs)
             except GitHubActionCaughtError:
+                issue_number = os.getenv('GH_ISSUE_NUMBER')
                 GitHubAction.add_labels_to_issue(issue_number, caught_error_labels)
                 raise
             except Exception as exception:
+                issue_number = os.getenv('GH_ISSUE_NUMBER')
                 GitHubAction.add_labels_to_issue(issue_number, uncaught_error_labels)
                 GitHubAction.add_error_comment_to_issue(issue_number,
                                                         uncaught_exception_msg_func(exception),

biosimulators_utils/image.py

@@ -54,15 +54,15 @@ def pull_docker_image(url):
             url, str(error).replace('\n', '\n  ')))
 
 
-def tag_and_push_docker_image(docker_client, image, tag):
+def tag_and_push_docker_image(image, tag):
     """ Tag and push Docker image
 
     Args:
-        docker_client (:obj:`docker.client.DockerClient`): Docker client
         image (:obj:`docker.models.images.Image`): Docker image
         tag (:obj:`str`): tag
     """
     assert image.tag(tag)
+    docker_client = docker.from_env()
     response = docker_client.images.push(tag)
     response = json.loads(response.rstrip().split('\n')[-1])
     if 'error' in response:

biosimulators_utils/simulator/io.py

@@ -39,7 +39,7 @@ def read_simulator_specs(url):
         specs = response.json()
     except simplejson.errors.JSONDecodeError as error:
         raise ValueError(''.join([
-            'Simulator specifications from {} could not be parsed.'.format(url),
+            'Simulator specifications from {} could not be parsed. '.format(url),
             'Specifications must be encoded into JSON.\n\n  {}'.format(str(error).replace('\n', '\n  ')),
         ]))
 
@@ -50,7 +50,7 @@ def read_simulator_specs(url):
         response.raise_for_status()
     except requests.RequestException as error:
         raise ValueError(''.join([
-            'Simulator specifications from {} are not valid.'.format(url),
+            'Simulator specifications from {} are not valid. '.format(url),
             'Specifications must be adhere to the BioSimulators schema. Documentation is available at {}.\n\n  {}'.format(
                 api_endpoint, str(error).replace('\n', '\n  ')),
         ]))

tests/gh_action/test_gh_action_core.py

@@ -111,8 +111,7 @@ def requests_delete_1(url, auth):
 
             # error handling: caught error
             class Action(GitHubAction):
-                @GitHubActionErrorHandling.catch_errors(GitHubAction.get_issue_number(),
-                                                        caught_error_labels=['invalid'],
+                @GitHubActionErrorHandling.catch_errors(caught_error_labels=['invalid'],
                                                         uncaught_error_labels=['action_error'])
                 def run(self):
                     raise GitHubActionCaughtError()
@@ -128,8 +127,7 @@ def requests_labels_method(url, headers, auth, json):
 
             # error handling: uncaught error
             class Action(GitHubAction):
-                @GitHubActionErrorHandling.catch_errors(GitHubAction.get_issue_number(),
-                                                        caught_error_labels=['invalid'],
+                @GitHubActionErrorHandling.catch_errors(caught_error_labels=['invalid'],
                                                         uncaught_error_labels=['action_error'])
                 def run(self):
                     raise ValueError('Details about error')

tests/test_image.py

@@ -37,7 +37,7 @@ def test_tag_and_push_docker_image(self):
         response = '{"error": "x"}'
         docker_client = mock.Mock(images=mock.Mock(push=lambda tag: response))
         with mock.patch('docker.from_env', return_value=docker_client):
-            with self.assertRaises(Exception):
+            with self.assertRaisesRegex(Exception, 'Unable to push image to'):
                 image.tag_and_push_docker_image(img, 'hello-world-2')
 
     def test_convert_docker_image_to_singularity(self):