EVA-3677 - Submission flow

eva_sub_cli/orchestrator.py

@@ -13,7 +13,8 @@
 from eva_sub_cli.exceptions.submission_not_found_exception import SubmissionNotFoundException
 from eva_sub_cli.exceptions.submission_status_exception import SubmissionStatusException
 from eva_sub_cli.submission_ws import SubmissionWSClient
-from eva_sub_cli.submit import StudySubmitter, SUB_CLI_CONFIG_KEY_SUBMISSION_ID
+from eva_sub_cli.submit import StudySubmitter, SUB_CLI_CONFIG_KEY_SUBMISSION_ID, \
+    SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL
 from eva_sub_cli.validators.docker_validator import DockerValidator
 from eva_sub_cli.validators.native_validator import NativeValidator
 from eva_sub_cli.validators.validator import READY_FOR_SUBMISSION_TO_EVA
@@ -131,11 +132,15 @@ def check_validation_required(tasks, sub_config, username=None, password=None):
     if SUBMIT in tasks:
         if not sub_config.get(READY_FOR_SUBMISSION_TO_EVA, False):
             return True
+        # If we are working with an existing submission check its status to see if it was submitted and failed before.
         submission_id = sub_config.get(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, None)
         if submission_id:
             try:
                 submission_status = SubmissionWSClient(username, password).get_submission_status(submission_id)
                 if submission_status == 'FAILED':
+                    # Reset the submission_id which will force the creation of a new one
+                    sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, value=None)
+                    sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL, value=None)
                     return True
                 else:
                     return False
@@ -151,7 +156,7 @@ def check_validation_required(tasks, sub_config, username=None, password=None):
                     raise SubmissionStatusException(f'Error occurred while getting status of the submission '
                                                     f'with Id {submission_id}')
 
-        logger.info(f'submission id not found in config. This might be the first time user is submitting')
+        logger.debug(f'submission id not found in config. This might be the first time user is submitting')
         return False
 
 

eva_sub_cli/submit.py

@@ -81,6 +81,13 @@ def _complete_submission(self):
         # update config with completion of the submission
         self.sub_config.set(SUB_CLI_CONFIG_KEY_COMPLETE, value=True)
 
+    def is_submission_status_open(self):
+        submission_id = self.sub_config.get(SUB_CLI_CONFIG_KEY_SUBMISSION_ID)
+        if submission_id:
+            status = self.submission_ws_client.get_submission_status(submission_id)
+            return status == 'OPEN'
+        return False
+
     def submit(self):
         if READY_FOR_SUBMISSION_TO_EVA not in self.sub_config or not self.sub_config[READY_FOR_SUBMISSION_TO_EVA]:
             raise Exception(f'There are still validation errors that need to be addressed. '
@@ -89,6 +96,12 @@ def submit(self):
             self.info(f'Initiate submission')
             self._initiate_submission()
 
+        if not self.is_submission_status_open():
+            self.warning(f'You requested the submission using {self.submission_dir}. '
+                         f'This contains directory an already completed submission. '
+                         f'Please create a new submission directory to resubmit.')
+            return
+
         # upload submission
         self.info(f'Upload data')
         self._upload_submission()

tests/test_orchestrator.py

@@ -11,7 +11,7 @@
 from eva_sub_cli.exceptions.submission_not_found_exception import SubmissionNotFoundException
 from eva_sub_cli.exceptions.submission_status_exception import SubmissionStatusException
 from eva_sub_cli.orchestrator import orchestrate_process, VALIDATE, SUBMIT, DOCKER, check_validation_required
-from eva_sub_cli.submit import SUB_CLI_CONFIG_KEY_SUBMISSION_ID
+from eva_sub_cli.submit import SUB_CLI_CONFIG_KEY_SUBMISSION_ID, SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL
 from eva_sub_cli.validators.validator import READY_FOR_SUBMISSION_TO_EVA
 from tests.test_utils import touch
 
@@ -47,30 +47,36 @@ def tearDown(self) -> None:
     def test_check_validation_required(self):
         tasks = ['submit']
 
-        sub_config = {READY_FOR_SUBMISSION_TO_EVA: False}
+        sub_config = WritableConfig(self.test_sub_dir, 'config.yaml')
+        sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=False)
         self.assertTrue(check_validation_required(tasks, sub_config))
 
-        sub_config = {READY_FOR_SUBMISSION_TO_EVA: True}
+        sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
+
         self.assertFalse(check_validation_required(tasks, sub_config))
 
         with patch('eva_sub_cli.submission_ws.SubmissionWSClient.get_submission_status') as get_submission_status_mock:
-            sub_config = {READY_FOR_SUBMISSION_TO_EVA: True,
-                          SUB_CLI_CONFIG_KEY_SUBMISSION_ID: 'test123'}
+            sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
+            sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, value='test123')
 
             get_submission_status_mock.return_value = 'OPEN'
             self.assertFalse(check_validation_required(tasks, sub_config))
 
             get_submission_status_mock.return_value = 'FAILED'
             self.assertTrue(check_validation_required(tasks, sub_config))
+            # A FAILD submission status reset the submission ID and submission URL
+            self.assertEqual(sub_config.get(SUB_CLI_CONFIG_KEY_SUBMISSION_ID), None)
+            self.assertEqual(sub_config.get(SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL), None)
+
+            sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
+            sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, value='test123')
 
-            mock_response = Mock()
-            mock_response.status_code = 404
+            mock_response = Mock(status_code=404)
             get_submission_status_mock.side_effect = HTTPError(response=mock_response)
             with self.assertRaises(SubmissionNotFoundException):
                 check_validation_required(tasks, sub_config)
 
-            mock_response = Mock()
-            mock_response.status_code = 500
+            mock_response = Mock(status_code=500)
             get_submission_status_mock.side_effect = HTTPError(response=mock_response)
             with self.assertRaises(SubmissionStatusException):
                 check_validation_required(tasks, sub_config)
@@ -96,7 +102,8 @@ def test_orchestrate_validate_submit(self):
                 patch('eva_sub_cli.orchestrator.WritableConfig') as m_config, \
                 patch('eva_sub_cli.orchestrator.get_project_title_and_create_vcf_files_mapping') as m_get_project_title_and_create_vcf_files_mapping, \
                 patch('eva_sub_cli.orchestrator.DockerValidator') as m_docker_validator, \
-                patch('eva_sub_cli.orchestrator.StudySubmitter') as m_submitter:
+                patch('eva_sub_cli.orchestrator.StudySubmitter') as m_submitter, \
+                patch('eva_sub_cli.orchestrator.check_validation_required', return_value=True):
             # Empty config
             config = WritableConfig()
             m_config.return_value = config

tests/test_submit.py

@@ -41,13 +41,15 @@ def test_submit(self):
         mock_initiate_response.status_code = 200
         mock_initiate_response.json.return_value = {"submissionId": "mock_submission_id",
                                                     "uploadUrl": "directory to use for upload"}
+
         mock_uploaded_response = MagicMock()
         mock_uploaded_response.status_code = 200
 
         test_submission_ws_client = SubmissionWSClient()
 
         with patch.object(test_submission_ws_client, 'auth') as mocked_auth:
             with patch.object(self.submitter, 'submission_ws_client', test_submission_ws_client), \
+                    patch.object(test_submission_ws_client, 'get_submission_status', return_value='OPEN'), \
                     patch('eva_sub_cli.submission_ws.requests.post', return_value=mock_initiate_response) as mock_post, \
                     patch('eva_sub_cli.submission_ws.requests.put', return_value=mock_uploaded_response) as mock_put, \
                     patch.object(StudySubmitter, '_upload_submission'), \
@@ -76,6 +78,7 @@ def test_submit_with_config(self):
         mock_uploaded_response.status_code = 200
 
         assert is_submission_dir_writable(self.test_sub_dir)
+        assert not os.path.exists(self.config_file)
         sub_config = WritableConfig(self.config_file, version='version1.0')
         sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
         sub_config.write()
@@ -84,6 +87,7 @@ def test_submit_with_config(self):
 
         with patch.object(test_submission_ws_client, 'auth') as mocked_auth:
             with patch.object(self.submitter, 'submission_ws_client', test_submission_ws_client), \
+                    patch.object(test_submission_ws_client, 'get_submission_status', return_value='OPEN'), \
                     patch('eva_sub_cli.submission_ws.requests.post', return_value=mock_initiate_response) as mock_post, \
                     patch('eva_sub_cli.submission_ws.requests.put', return_value=mock_uploaded_response) as mock_put, \
                     patch.object(StudySubmitter, '_upload_submission'):
@@ -100,6 +104,24 @@ def test_submit_with_config(self):
             assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_ID] == "mock_submission_id"
             assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL] == "directory to use for upload"
 
+    def test_submit_when_already_completed(self):
+        test_submission_ws_client = SubmissionWSClient()
+
+        with patch.object(self.submitter, 'submission_ws_client', test_submission_ws_client), \
+                patch.object(test_submission_ws_client, 'get_submission_status', return_value='UPLOADED') as mock_get_submission_status, \
+                patch.object(self.submitter, 'submission_dir', self.test_sub_dir), \
+                patch.object(self.submitter, '_initiate_submission') as mock_initiate, \
+                patch.object(self.submitter, '_upload_submission') as mock_upload, \
+                patch.object(self.submitter, '_complete_submission') as mock_complete:
+
+            self.submitter.sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
+            self.submitter.sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL, value='directory to use for upload')
+            self.submitter.submit()
+            # No call was made to the end point or the upload because the submission status is 'UPLOADED'
+            mock_initiate.assert_not_called()
+            mock_upload.assert_not_called()
+            mock_complete.assert_not_called()
+
     def test_sub_config_file_creation(self):
         assert is_submission_dir_writable(self.test_sub_dir)
         self.submitter.sub_config.set('test_key', value='test_value')