From 276e27fe59c60e4b5569bfab8e99a0c7738110ca Mon Sep 17 00:00:00 2001
From: tcezard <tcezard@ebi.ac.uk>
Date: Fri, 20 Dec 2024 12:05:17 +0000
Subject: [PATCH] Lock file was specified instead of the locked directory.

---
 eva_sub_cli/executables/cli.py |  9 ++++++++-
 tests/test_cli.py              | 23 +++++++++++++++++++----
 2 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/eva_sub_cli/executables/cli.py b/eva_sub_cli/executables/cli.py
index db8c0c4..42c6495 100755
--- a/eva_sub_cli/executables/cli.py
+++ b/eva_sub_cli/executables/cli.py
@@ -79,6 +79,7 @@ def parse_args(cmd_line_args):
 
 
 def main():
+    exit_status = 0
     args = parse_args(sys.argv[1:])
 
     args.submission_dir = os.path.abspath(args.submission_dir)
@@ -91,7 +92,7 @@ def main():
     try:
         # lock the submission directory
 
-        with DirLock(os.path.join(args.submission_dir, '.lock')) as lock:
+        with DirLock(os.path.join(args.submission_dir)) as lock:
             # Create the log file
             logging_config.add_file_handler(os.path.join(args.submission_dir, 'eva_submission.log'), logging.DEBUG)
             # Pass on all the arguments to the orchestrator
@@ -100,9 +101,15 @@ def main():
         print(f'Could not acquire the lock file for {args.submission_dir} because another process is using this '
               f'directory or a previous process did not terminate correctly. '
               f'If the problem persists, remove the lock file manually.')
+        exit_status = 65
     except FileNotFoundError as fne:
         print(fne)
+        exit_status = 66
     except SubmissionNotFoundException as snfe:
         print(f'{snfe}. Please contact EVA Helpdesk')
+        exit_status = 67
     except SubmissionStatusException as sse:
         print(f'{sse}. Please try again later. If the problem persists, please contact EVA Helpdesk')
+        exit_status = 68
+    return exit_status
+
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 2381cdc..8056c7c 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,5 +1,7 @@
 import copy
 import logging
+import os
+import shutil
 import sys
 from unittest import TestCase
 from unittest.mock import patch, Mock
@@ -11,19 +13,31 @@
 
 class TestCli(TestCase):
 
+    resources_folder = os.path.join(os.path.dirname(__file__), 'resources')
+    submission_dir = os.path.abspath(os.path.join(resources_folder, 'submission_dir'))
+
+    def setUp(self) -> None:
+        os.makedirs(self.submission_dir, exist_ok=True)
+
+    def tearDown(self) -> None:
+        if os.path.exists(self.submission_dir):
+            shutil.rmtree(self.submission_dir)
+
     def test_main(self):
-        args = Mock(submission_dir='.', vcf_files=[], reference_fasta='', metadata_json=None, metadata_xlsx='',
+        args = Mock(submission_dir=self.submission_dir,
+                    vcf_files=[], reference_fasta='', metadata_json=None, metadata_xlsx='',
                     tasks='validate', executor='native', debug=False)
         with patch('eva_sub_cli.executables.cli.parse_args', return_value=args), \
                 patch('eva_sub_cli.orchestrator.orchestrate_process'):
-            cli.main()
+            exit_status = cli.main()
             # Check that the debug message is shown
             logger = orchestrator.logger
             logger.debug('test')
+            assert exit_status == 0
 
     def test_validate_args(self):
         cmd_args = [
-            '--submission_dir', '.',
+            '--submission_dir', self.submission_dir,
             '--vcf_files', 'test.vcf',
             '--reference_fasta', 'test.fasta',
             '--metadata_json', 'test.json',
@@ -32,9 +46,10 @@ def test_validate_args(self):
             '--debug'
         ]
         args = cli.parse_args(cmd_args)
-        assert args.submission_dir == '.'
+        assert args.submission_dir == self.submission_dir
 
 
         with patch('sys.exit') as m_exit:
             cli.parse_args(cmd_args[:2]+cmd_args[4:])
             m_exit.assert_called_once_with(1)
+