review comments

cli/eva_sub_cli.py

@@ -26,13 +26,13 @@ def get_docker_validator(vcf_files_mapping, output_dir, metadata_json, metadata_
 
 
 if __name__ == "__main__":
-    argparser = ArgumentParser(description='EVA SUB CLI - to validate and submit a submission')
+    argparser = ArgumentParser(description='EVA Submission CLI - validate and submit data to EVA')
     argparser.add_argument('--task', required=True, choices=[VALIDATE, SUBMIT, RESUME],
                            help='Select a task to perform')
     argparser.add_argument('--submission_dir', required=True, type=str,
                            help='Full path to the directory where all processing will be done and submission info is/will be stored')
-    argparser.add_argument("--docker_path", help="Full path to the docker installation, "
-                                                 "not required if docker is available on path", required=False)
+    argparser.add_argument("--docker_path", required=False, help="Full path to the docker installation, "
+                                                "not required if docker is available in the PATH environment variable")
     argparser.add_argument("--container_name", help="Name of the docker container", required=False)
     argparser.add_argument("--vcf_files_mapping", required=False,
                            help="csv file with the mappings for vcf files, fasta and assembly report")
@@ -54,7 +54,8 @@ def get_docker_validator(vcf_files_mapping, output_dir, metadata_json, metadata_
 
     if args.task == VALIDATE or args.task == SUBMIT:
         if not args.vcf_files_mapping:
-            raise Exception(f"Please provide csv file with the mappings of vcf files using --vcf_files_mapping")
+            raise Exception(f"Please provide a CSV file which provides VCF and corresponding assembly information "
+                            f"(use the --vcf_files_mapping switch)")
         if not args.metadata_json and not args.metadata_xlsx:
             raise Exception(f"Please provide the file that describes the project, analysis, samples and files "
                             f"using either --metadata_json or --metadata_xlsx")

cli/submit.py

@@ -28,6 +28,7 @@ def __init__(self, submission_dir, submission_initiate_url=SUBMISSION_INITIATE_U
     def update_config_with_submission_id_and_upload_url(self, submission_id, upload_url):
         self.sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, value=submission_id)
         self.sub_config.set(SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL, value=upload_url)
+        self.sub_config.backup()
         self.sub_config.write()
 
     # TODO
@@ -36,7 +37,8 @@ def upload_submission(self, submission_id=None, submission_upload_url=None):
             raise Exception(f'Cannot resume submission. Config file is empty')
 
         if not self.sub_config[READY_FOR_SUBMISSION_TO_EVA]:
-            raise Exception(f'There are still validation errors that needs to be fixed. Please fix them before uploading')
+            raise Exception(f'There are still validation errors that needs to be addressed. '
+                            f'Please review, address and re-validate before uploading.')
 
         if not submission_id or not submission_upload_url:
             submission_id = self.sub_config[SUB_CLI_CONFIG_KEY_SUBMISSION_ID]
@@ -51,7 +53,8 @@ def verify_submission_dir(self, submission_dir):
 
     def submit(self, submission_dir):
         if not self.sub_config[READY_FOR_SUBMISSION_TO_EVA]:
-            raise Exception(f'There are still validation errors that needs to be fixed. Please fix them before submitting.')
+            raise Exception(f'There are still validation errors that need to be addressed. '
+                            f'Please review, address and re-validate before submitting.')
 
         self.verify_submission_dir(submission_dir)
         response = requests.post(self.submission_initiate_url,

tests/test_submit.py

@@ -59,6 +59,8 @@ def test_submit(self):
             "submissionId": "mock_submission_id",
             "uploadUrl": "directory to use for upload",
         }
+
+        self.submitter.verify_submission_dir(self.test_sub_dir)
         sub_config = WritableConfig(self.config_file, version='version1.0')
         sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
         sub_config.write()
@@ -68,6 +70,8 @@ def test_submit(self):
 
         assert os.path.exists(self.test_sub_dir)
         assert os.path.exists(self.config_file)
+        # assert backup file is created
+        assert os.path.exists(f"{self.config_file}.1")
         with (open(self.config_file, 'r') as f):
             sub_config_data = yaml.safe_load(f)
             assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_ID] == "mock_submission_id"