Merge pull request #136 from seqeralabs/error_catching

fix: catch errors more reliably

seqerakit/seqeraplatform.py

@@ -96,8 +96,8 @@ def _execute_command(self, full_cmd, to_json=False):
         stdout, _ = process.communicate()
         stdout = stdout.decode("utf-8").strip()
 
-        if "ERROR: " in stdout:
-            self._handle_command_errors(stdout)
+        if "ERROR: " in stdout or process.returncode != 0:
+            self._handle_command_errors(str(stdout))
 
         return json.loads(stdout) if to_json else stdout
 
@@ -114,11 +114,11 @@ def _handle_command_errors(self, stdout):
             r"ERROR: .*already (exists|a participant)", stdout, flags=re.IGNORECASE
         ):
             raise ResourceExistsError(
-                " Resource already exists. Please delete first or set 'overwrite: true'"
+                "Resource already exists. Please delete first or set 'overwrite: true'"
             )
         else:
             raise ResourceCreationError(
-                f" Resource creation failed: '{stdout}'. "
+                f"Resource creation failed: '{stdout}'. "
                 "Check your config and try again."
             )
 

tests/unit/test_seqeraplatform.py

@@ -1,5 +1,5 @@
 import unittest
-from unittest.mock import patch
+from unittest.mock import MagicMock, patch
 from seqerakit import seqeraplatform
 import json
 import subprocess
@@ -26,6 +26,7 @@ def test_run_with_jsonout_command(self, mock_subprocess):
             "dateCreated": "2023-02-15T13:14:30Z",
         }
         # Mock the stdout of the Popen process
+        mock_subprocess.return_value = MagicMock(returncode=0)
         mock_subprocess.return_value.communicate.return_value = (
             json.dumps(mock_pipelines_json).encode(),
             b"",
@@ -93,6 +94,7 @@ def test_resource_creation_error(self):
     def test_json_parsing(self):
         with patch("subprocess.Popen") as mock_subprocess:
             # Mock the stdout of the Popen process to return JSON
+            mock_subprocess.return_value = MagicMock(returncode=0)
             mock_subprocess.return_value.communicate.return_value = (
                 b'{"key": "value"}',
                 b"",
@@ -112,6 +114,7 @@ def setUp(self):
     @patch("subprocess.Popen")
     def test_cli_args_inclusion(self, mock_subprocess):
         # Mock the stdout of the Popen process
+        mock_subprocess.return_value = MagicMock(returncode=0)
         mock_subprocess.return_value.communicate.return_value = (
             json.dumps({"key": "value"}).encode(),
             b"",
@@ -136,6 +139,7 @@ def test_cli_args_inclusion_ssl_certs(self, mock_subprocess):
         seqeraplatform.SeqeraPlatform(cli_args=self.cli_args)
 
         # Mock the stdout of the Popen process
+        mock_subprocess.return_value = MagicMock(returncode=0)
         mock_subprocess.return_value.communicate.return_value = (
             json.dumps({"key": "value"}).encode(),
             b"",