1366 update exit code

README.md

@@ -154,7 +154,7 @@ Run `python core.py validate --help` to see the list of validation options.
                                   --output-format JSON.
   -dv, --define-version TEXT      Define-XML version used for validation
   -dxp, --define-xml-path         Path to define-xml file.
-  -vx, --validate-xml             This flag enables XML validation against a Define-XML schema.
+  -vx, --validate-xml             Enable XML validation (default 'y' to enable, otherwise disable).
   --whodrug TEXT                  Path to directory with WHODrug dictionary
                                   files
   --meddra TEXT                   Path to directory with MedDRA dictionary

core.py

@@ -207,8 +207,8 @@ def cli():
 @click.option(
     "-vx",
     "--validate-xml",
-    is_flag=True,
-    help="This flag enables XML validation against a Define-XML schema.",
+    default="y",
+    help="Enable XML validation (default 'y' to enable, otherwise disable)",
 )
 @click.pass_context
 def validate(
@@ -241,7 +241,7 @@ def validate(
     custom_standard: bool,
     progress: str,
     define_xml_path: str,
-    validate_xml: bool,
+    validate_xml: str,
 ):
     """
     Validate data using CDISC Rules Engine
@@ -259,7 +259,11 @@ def validate(
             logger.error(
                 "Flag --raw-report can be used only when --output-format is JSON"
             )
-            ctx.exit()
+            ctx.exit(2)
+
+    if exclude_rules and rules:
+        logger.error("Cannot use both --rules and --exclude-rules flags together.")
+        ctx.exit(2)
 
     if exclude_rules and rules:
         logger.error("Cannot use both --rules and --exclude-rules flags together.")
@@ -287,28 +291,29 @@ def validate(
             logger.error(
                 "Argument --dataset-path cannot be used together with argument --data"
             )
-            ctx.exit()
+            ctx.exit(2)
         dataset_paths, found_formats = valid_data_file(
             [str(Path(data).joinpath(fn)) for fn in os.listdir(data)]
         )
         if len(found_formats) > 1:
             logger.error(
                 f"Argument --data contains more than one allowed file format ({', '.join(found_formats)})."  # noqa: E501
             )
-            ctx.exit()
+            ctx.exit(2)
     elif dataset_path:
         dataset_paths, found_formats = valid_data_file([dp for dp in dataset_path])
         if len(found_formats) > 1:
             logger.error(
                 f"Argument --dataset-path contains more than one allowed file format ({', '.join(found_formats)})."  # noqa: E501
             )
-            ctx.exit()
+            ctx.exit(2)
     else:
         logger.error(
             "You must pass one of the following arguments: --dataset-path, --data"
         )
         # no need to define dataset_paths here, the program execution will stop
-        ctx.exit()
+        ctx.exit(2)
+    validate_xml_bool = True if validate_xml.lower() in ("y", "yes") else False
     run_validation(
         Validation_args(
             cache_path,
@@ -331,7 +336,7 @@ def validate(
             custom_standard,
             progress,
             define_xml_path,
-            validate_xml,
+            validate_xml_bool,
         )
     )
 

scripts/script_utils.py

@@ -49,16 +49,18 @@ def get_library_metadata_from_cache(args) -> LibraryMetadataContainer:  # noqa
             define_version.model_package == "define_2_1"
             and len(args.controlled_terminology_package) > 0
         ):
-            raise ValueError(
+            engine_logger.error(
                 "Cannot use -ct controlled terminology package command with Define-XML2.1 submission"
             )
+            raise SystemError(2)
         elif (
             define_version.model_package == "define_2_0"
             and len(args.controlled_terminology_package) > 1
         ):
-            raise ValueError(
+            engine_logger.error(
                 "Cannot provide multiple controlled terminology packages with Define-XML2.0 submission"
             )
+            raise SystemError(2)
     standards_file = os.path.join(args.cache, "standards_details.pkl")
     models_file = os.path.join(args.cache, "standards_models.pkl")
     variables_codelist_file = os.path.join(args.cache, "variable_codelist_maps.pkl")

tests/QARegressionTests/test_core/test_validate.py

@@ -232,7 +232,7 @@ def test_validate_include_exclude(self):
             "CORE-000473",
         ]
         exit_code, stdout, stderr = run_command(args, False)
-        self.assertEqual(exit_code, 0)
+        self.assertEqual(exit_code, 2)
         self.assertIn(
             "cannot use both --rules and --exclude-rules flags together.", stderr
         )
@@ -534,7 +534,7 @@ def test_validate_dummy_with_all_options(self):
             f"-l error"
         )
         exit_code, stdout, stderr = run_command(args, True)
-        self.assertEqual(exit_code, 0)
+        self.assertEqual(exit_code, 2)
         self.assertFalse(self.error_keyword in stdout)
         self.assertFalse(self.error_keyword in stdout)
         expected_pattern = (
@@ -558,7 +558,7 @@ def test_validate_dummy_without_dataset_path(self):
             f"-v 3.4 "
         )
         exit_code, stdout, stderr = run_command(args, True)
-        self.assertEqual(exit_code, 0)
+        self.assertEqual(exit_code, 2)
         expected_pattern = (
             r"\[error \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2},\d{3} - "
             r"core\.py:\d+\] - you must pass one of the following arguments: "
@@ -611,27 +611,28 @@ def test_validate_dummy_with_invalid_whodrug_and_meddra(self):
         self.assertNotEqual(exit_code, 0)
         self.assertNotEqual(stderr, "", f"Error while executing command:\n{stderr}")
 
-    def test_validate_dummy_without_vx(self):
+    def test_validate_dummy_with_vx_as_no(self):
         args = (
             f"python core.py validate "
             f"-s sendig "
             f"-v 3.1 "
             f"-dv 2.1 "
             f"-lr {os.path.join('tests', 'resources', 'CoreIssue295', 'SEND4.json')} "
             f"-dp {os.path.join('tests', 'resources', 'CoreIssue295', 'dm.json')} "
+            f"-vx no"
         )
         exit_code, stdout, stderr = run_command(args, True)
         self.assertNotIn("error", stdout)
 
-    def test_validate_dummy_with_vx(self):
+    def test_validate_dummy_with_vx_as_yes(self):
         args = (
             f"python core.py validate "
             f"-s sendig "
             f"-v 3.1 "
             f"-dv 2.1 "
             f"-lr {os.path.join('tests', 'resources', 'CoreIssue295', 'SEND4.json')} "
             f"-dp {os.path.join('tests', 'resources', 'CoreIssue295', 'dm.json')} "
-            f"-vx"
+            f"-vx y"
         )
         exit_code, stdout, stderr = run_command(args, True)
         self.assertEqual(exit_code, 0)