Couple of fixes

eva_sub_cli/orchestrator.py

@@ -155,7 +155,7 @@ def orchestrate_process(submission_dir, vcf_files, reference_fasta, metadata_jso
 
     metadata_file = metadata_json or metadata_xlsx
     if not os.path.exists(os.path.abspath(metadata_file)):
-        raise FileNotFoundError(f'The provided metadata file {metadata_file} does not exist')
+        raise FileNotFoundError(f'The provided metadata file {os.path.abspath(metadata_file)} does not exist')
 
     if metadata_json:
         metadata_json = os.path.abspath(metadata_json)

eva_sub_cli/submit.py

@@ -64,7 +64,8 @@ def _upload_submission(self):
     def _upload_file(self, submission_upload_url, input_file):
         base_name = os.path.basename(input_file)
         self.debug(f'Transfer {base_name} to EVA FTP')
-        r = requests.put(os.path.join(submission_upload_url, base_name), data=open(input_file, 'rb'))
+        with open(input_file, 'rb') as f:
+            r = requests.put(os.path.join(submission_upload_url, base_name), data=open(input_file, 'rb'))
         r.raise_for_status()
         self.debug(f'Upload of {base_name} completed')
 

eva_sub_cli/validators/docker_validator.py

@@ -12,7 +12,7 @@
 logger = logging_config.get_logger(__name__)
 
 container_image = 'ebivariation/eva-sub-cli'
-container_tag = 'v0.0.1.dev14'
+container_tag = 'v0.0.1.dev15'
 container_validation_dir = '/opt/vcf_validation'
 container_validation_output_dir = 'vcf_validation_output'
 

eva_sub_cli/validators/native_validator.py

@@ -24,11 +24,15 @@ def _validate(self):
 
     def run_validator(self):
         self.verify_executables_installed()
+        curr_wd = os.getcwd()
         try:
             command = self.get_validation_cmd()
+            os.chdir(self.submission_dir)
             self._run_quiet_command("Run Validation using Nextflow", command)
         except subprocess.CalledProcessError as ex:
             logger.error(ex)
+        finally:
+            os.chdir(curr_wd)
 
     def get_validation_cmd(self):
         if self.metadata_xlsx and not self.metadata_json:

tests/test_orchestrator.py

@@ -239,11 +239,13 @@ def test_orchestrate_with_metadata_xlsx(self):
             )
             m_docker_validator().validate_and_report.assert_called_once_with()
 
-
     def test_metadata_file_does_not_exist_error(self):
         with self.assertRaises(Exception) as context:
-            orchestrate_process(self.test_sub_dir, None, None, None, self.metadata_xlsx,
-                    tasks=[VALIDATE], executor=DOCKER)
-        self.assertRegex(str(context.exception),r"The provided metadata file .*/resources/test_sub_dir/sub_metadata.xlsx does not exist")
+            orchestrate_process(self.test_sub_dir, None, None, None, 'Non_existing_metadata.xlsx',
+                                tasks=[VALIDATE], executor=DOCKER)
+        self.assertRegex(
+            str(context.exception),
+            r"The provided metadata file .*/resources/test_sub_dir/Non_existing_metadata.xlsx does not exist"
+        )