update regression tests and run them in CI tests

.github/workflows/test-unit.yml

@@ -24,4 +24,3 @@ jobs:
         run: |
           python -m pytest tests/unit/ --cov=cdisc_rules_engine --cov-fail-under=75
           python -m pytest tests/QARegressionTests/
-          python -m pytest -m regression tests/QARegressionTests/test_Issues

tests/QARegressionTests/globals.py

@@ -1,10 +1,10 @@
-issue_datails_sheet = "Issue Details"
-dataset_details_sheet = "Dataset Details"
-entity_details_sheet = "Entity Details"
-rules_report_sheet = "Rules Report"
-issue_sheet_coreid_column = "A"
-dataset_sheet_dataset_column = "A"
-rules_sheet_rule_status_column = "F"
-issue_sheet_record_column = "G"
-issue_sheet_variable_column = "I"
-issue_sheet_values_column = "J"
+issue_datails_sheet = "Issue Details"
+dataset_details_sheet = "Dataset Details"
+entity_details_sheet = "Entity Details"
+rules_report_sheet = "Rules Report"
+issue_sheet_coreid_column = "A"
+dataset_sheet_dataset_column = "A"
+rules_sheet_rule_status_column = "F"
+issue_sheet_record_column = "F"
+issue_sheet_variable_column = "H"
+issue_sheet_values_column = "I"

tests/QARegressionTests/test_Issues/test_CoreIssue1023.py

@@ -1,57 +1,56 @@
-import os
-import subprocess
-import json
-
-import pytest
-from conftest import get_python_executable
-
-
-@pytest.mark.regression
-class TestCoreIssue1023:
-
-    def test_dataset_utf8(self):
-        """Test that the engine correctly handles dataset files with utf8 encoding"""
-        command = [
-            f"{get_python_executable()}",
-            "-m",
-            "core",
-            "validate",
-            "-s",
-            "sdtmig",
-            "-v",
-            "3.4",
-            "-r",
-            "CORE-000766",
-            "-e",
-            "utf8",
-            "-dp",
-            os.path.join("tests", "resources", "CoreIssue1023", "ae_utf8.json"),
-            "--output-format",
-            "json",
-        ]
-        subprocess.run(command, check=True)
-
-        files = os.listdir()
-        json_files = [
-            file
-            for file in files
-            if file.startswith("CORE-Report-") and file.endswith(".json")
-        ]
-        json_report_path = sorted(json_files)[-1]
-        # Open the JSON report file
-        json_report = json.load(open(json_report_path, "r", encoding="utf8"))
-        assert {
-            "Conformance_Details",
-            "Dataset_Details",
-            "Issue_Summary",
-            "Issue_Details",
-            "Rules_Report",
-        }.issubset(json_report.keys())
-        datasets = {x["filename"] for x in json_report["Dataset_Details"]}
-        assert datasets == {"AE"}
-        assert (
-            json_report["Issue_Details"][0]["USUBJID"]
-            == f"utf8:{b'\xe1\xbc\x87'.decode('utf8')}"
-        )
-        if os.path.exists(json_report_path):
-            os.remove(json_report_path)
+import os
+import subprocess
+import json
+
+from conftest import get_python_executable
+
+
+class TestCoreIssue1023:
+
+    def test_dataset_utf8(self):
+        """Test that the engine correctly handles dataset files with utf8
+        encoding."""
+        command = [
+            f"{get_python_executable()}",
+            "-m",
+            "core",
+            "validate",
+            "-s",
+            "sdtmig",
+            "-v",
+            "3.4",
+            "-lr",
+            os.path.join("tests", "resources", "library_rules", "CORE-000766.json"),
+            "-e",
+            "utf8",
+            "-dp",
+            os.path.join("tests", "resources", "CoreIssue1023", "ae_utf8.json"),
+            "--output-format",
+            "json",
+        ]
+        subprocess.run(command, check=True)
+
+        files = os.listdir()
+        json_files = [
+            file
+            for file in files
+            if file.startswith("CORE-Report-") and file.endswith(".json")
+        ]
+        json_report_path = sorted(json_files)[-1]
+        # Open the JSON report file
+        json_report = json.load(open(json_report_path, "r", encoding="utf8"))
+        assert {
+            "Conformance_Details",
+            "Dataset_Details",
+            "Issue_Summary",
+            "Issue_Details",
+            "Rules_Report",
+        }.issubset(json_report.keys())
+        datasets = {x["filename"] for x in json_report["Dataset_Details"]}
+        assert datasets == {"AE"}
+        assert (
+            json_report["Issue_Details"][0]["USUBJID"]
+            == f"utf8:{b'\xe1\xbc\x87'.decode('utf8')}"
+        )
+        if os.path.exists(json_report_path):
+            os.remove(json_report_path)

tests/QARegressionTests/test_Issues/test_CoreIssue1204.py

@@ -1,40 +1,38 @@
-import subprocess
-import pytest
-from conftest import get_python_executable
-
-
-@pytest.mark.regression
-def test_non_existing_dataset_shows_helpful_error():
-    """Test that the engine displays a helpful error message if dataset files are not found"""
-    command = [
-        get_python_executable(),
-        "-m",
-        "core",
-        "validate",
-        "-s",
-        "sdtmig",
-        "-v",
-        "3.4",
-        "-dp",
-        "ds.json",
-        "-dp",
-        "ds2.json",
-    ]
-
-    process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    stdout, stderr = process.communicate()
-
-    stderr_text = stderr.decode()
-    stdout_text = stdout.decode()
-
-    assert process.returncode == 2, "Expected non-zero exit code"
-    assert (
-        "FileNotFoundError" not in stderr_text
-    ), "Should not show FileNotFoundError crash"
-    assert (
-        "Failed to execute script" not in stderr_text
-    ), "Should not show script execution failure"
-    assert "Files ds.json, ds2.json are not found" in stderr_text, (
-        f"Expected helpful error message about non-existing dataset files. "
-        f"stderr: {stderr_text}, stdout: {stdout_text}"
-    )
+import subprocess
+from conftest import get_python_executable
+
+
+def test_non_existing_dataset_shows_helpful_error():
+    """Test that the engine displays a helpful error message if dataset files are not found"""
+    command = [
+        get_python_executable(),
+        "-m",
+        "core",
+        "validate",
+        "-s",
+        "sdtmig",
+        "-v",
+        "3.4",
+        "-dp",
+        "ds.json",
+        "-dp",
+        "ds2.json",
+    ]
+
+    process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    stdout, stderr = process.communicate()
+
+    stderr_text = stderr.decode()
+    stdout_text = stdout.decode()
+
+    assert process.returncode == 2, "Expected non-zero exit code"
+    assert (
+        "FileNotFoundError" not in stderr_text
+    ), "Should not show FileNotFoundError crash"
+    assert (
+        "Failed to execute script" not in stderr_text
+    ), "Should not show script execution failure"
+    assert "Files ds.json, ds2.json are not found" in stderr_text, (
+        f"Expected helpful error message about non-existing dataset files. "
+        f"stderr: {stderr_text}, stdout: {stdout_text}"
+    )