From 6d540e6864d918a2a442135e885589aad84ebf73 Mon Sep 17 00:00:00 2001
From: nkumar2 <nkumar2@ebi.ac.uk>
Date: Fri, 6 Oct 2023 12:37:48 +0100
Subject: [PATCH] add version to config

---
 cli/docker_validator.py | 8 ++++----
 cli/eva_sub_cli.py      | 6 +++---
 cli/submit.py           | 6 +++---
 tests/test_submit.py    | 4 ++--
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/cli/docker_validator.py b/cli/docker_validator.py
index abe6c3f..740d1ab 100644
--- a/cli/docker_validator.py
+++ b/cli/docker_validator.py
@@ -4,12 +4,12 @@
 import subprocess
 import time
 
-from cli import ETC_DIR, SUB_CLI_CONFIG_FILE
+from ebi_eva_common_pyutils.WritableConfig import WritableConfig
+
+from cli import ETC_DIR, SUB_CLI_CONFIG_FILE, __version__
 from cli.reporter import Reporter
 from ebi_eva_common_pyutils.logger import logging_config
 
-from cli.writable_config import WritableConfig
-
 logger = logging_config.get_logger(__name__)
 
 docker_path = 'docker'
@@ -65,7 +65,7 @@ def __init__(self, mapping_file, output_dir, metadata_json=None, metadata_xlsx=N
             self.sub_config = submission_config
         else:
             config_file = os.path.join(output_dir, SUB_CLI_CONFIG_FILE)
-            self.sub_config = WritableConfig(config_file)
+            self.sub_config = WritableConfig(config_file, version=__version__)
         super().__init__(self._find_vcf_file(), output_dir)
 
     def _validate(self):
diff --git a/cli/eva_sub_cli.py b/cli/eva_sub_cli.py
index 32cedf5..80d90c0 100644
--- a/cli/eva_sub_cli.py
+++ b/cli/eva_sub_cli.py
@@ -1,12 +1,12 @@
 import os
 from argparse import ArgumentParser
 
+from ebi_eva_common_pyutils.WritableConfig import WritableConfig
 from ebi_eva_common_pyutils.logger import logging_config
 
-from cli import SUB_CLI_CONFIG_FILE
+from cli import SUB_CLI_CONFIG_FILE, __version__
 from cli.docker_validator import DockerValidator, docker_path, container_image
 from cli.submit import StudySubmitter
-from cli.writable_config import WritableConfig
 
 VALIDATION_OUTPUT_DIR = "validation_output"
 VALIDATE = 'validate'
@@ -46,7 +46,7 @@ def get_docker_validator(vcf_files_mapping, output_dir, metadata_json, metadata_
 
     # load config
     config_file_path = os.path.join(args.submission_dir, SUB_CLI_CONFIG_FILE)
-    sub_config = WritableConfig(config_file_path)
+    sub_config = WritableConfig(config_file_path, version=__version__)
 
     if args.task == RESUME:
         submitter = StudySubmitter(args.submission_dir, submission_config=sub_config)
diff --git a/cli/submit.py b/cli/submit.py
index ede00b9..83712f7 100644
--- a/cli/submit.py
+++ b/cli/submit.py
@@ -2,12 +2,12 @@
 import os
 
 import requests
+from ebi_eva_common_pyutils.WritableConfig import WritableConfig
 from ebi_eva_common_pyutils.logger import logging_config
 
-from cli import SUB_CLI_CONFIG_FILE
+from cli import SUB_CLI_CONFIG_FILE, __version__
 from cli.auth import get_auth
 from cli.docker_validator import READY_FOR_SUBMISSION_TO_EVA
-from cli.writable_config import WritableConfig
 
 logger = logging_config.get_logger(__name__)
 SUB_CLI_CONFIG_KEY_SUBMISSION_ID = "submission_id"
@@ -23,7 +23,7 @@ def __init__(self, submission_dir, submission_initiate_url=SUBMISSION_INITIATE_U
             self.sub_config = submission_config
         else:
             config_file = os.path.join(submission_dir, SUB_CLI_CONFIG_FILE)
-            self.sub_config = WritableConfig(config_file)
+            self.sub_config = WritableConfig(config_file, version=__version__)
 
     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)
diff --git a/tests/test_submit.py b/tests/test_submit.py
index 37c36c3..1225c37 100644
--- a/tests/test_submit.py
+++ b/tests/test_submit.py
@@ -5,13 +5,13 @@
 from unittest.mock import MagicMock, patch, Mock, PropertyMock
 
 import yaml
+from ebi_eva_common_pyutils.WritableConfig import WritableConfig
 
 from cli import LSRI_CLIENT_ID
 from cli.auth import WebinAuth, LSRIAuth
 from cli.docker_validator import READY_FOR_SUBMISSION_TO_EVA
 from cli.eva_sub_cli import SUB_CLI_CONFIG_FILE
 from cli.submit import StudySubmitter, SUB_CLI_CONFIG_KEY_SUBMISSION_ID, SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL
-from cli.writable_config import WritableConfig
 
 
 class TestSubmit(unittest.TestCase):
@@ -59,7 +59,7 @@ def test_submit(self):
             "submissionId": "mock_submission_id",
             "uploadUrl": "directory to use for upload",
         }
-        sub_config = WritableConfig(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()