688: update tests

.github/workflows/test-suite.yml

@@ -35,7 +35,6 @@ jobs:
       - name: Install dependencies
         run: |
           pip install -r requirements.txt
-
       - name: Update rules cache
         env:
           CDISC_LIBRARY_API_KEY: ${{ secrets.CDISC_LIBRARY_API_KEY }}

.github/workflows/test-unit.yml

@@ -17,9 +17,11 @@ jobs:
       - name: Install requirements
         run: |
           pip install -r requirements-dev.txt
+          pip install -e .
       - name: Running Tests
         env:
           CDISC_LIBRARY_API_KEY: fakekey12341234
         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

@@ -1,5 +1,6 @@
 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"

tests/QARegressionTests/test_Issues/test_CoreIssue1326.py

@@ -5,7 +5,7 @@
 import pytest
 from conftest import get_python_executable
 from QARegressionTests.globals import (
-    dataset_details_sheet,
+    entity_details_sheet,
     issue_datails_sheet,
     rules_report_sheet,
     issue_sheet_record_column,
@@ -81,7 +81,7 @@ def test_positive_dataset(self):
         if os.path.exists(excel_file_path):
             os.remove(excel_file_path)
 
-    def test_negaive_dataset(self):
+    def test_negative_dataset(self):
         # Run the command in the terminal
         command = [
             f"{get_python_executable()}",
@@ -115,12 +115,12 @@ def test_negaive_dataset(self):
         # # Open the Excel file
         workbook = openpyxl.load_workbook(excel_file_path)
 
-        # --- Dataset Details ---
-        dataset_sheet = workbook[dataset_details_sheet]
+        # --- Entity Details ---
+        dataset_sheet = workbook[entity_details_sheet]
         dataset_values = [row for row in dataset_sheet.iter_rows(values_only=True)][1:]
         dataset_values = [row for row in dataset_values if any(row)]
         assert len(dataset_values) > 0
-        assert dataset_values[0][0] == "StudyVersion.xpt"
+        assert dataset_values[0][0] == "StudyVersion"
         assert dataset_values[0][-1] == 7
 
         # --- Issue Summary ---
@@ -131,7 +131,7 @@ def test_negaive_dataset(self):
         summary_values = [row for row in summary_values if any(row)]
         assert len(summary_values) > 0
         assert summary_values[0][1] == "CORE-000409"
-        assert summary_values[0][3] == 7
+        assert summary_values[0][4] == 7
 
         # --- Issue Details ---
         expected_values = [
@@ -159,7 +159,7 @@ def test_negaive_dataset(self):
         rules_values = [row for row in rules_values if any(row)]
         assert len(rules_values) > 0
         assert rules_values[0][0] == "CORE-000409"
-        assert rules_values[0][-1] == "SUCCESS"
+        assert rules_values[0][-1] == "ISSUE REPORTED"
 
         if os.path.exists(excel_file_path):
             os.remove(excel_file_path)

tests/QARegressionTests/test_Issues/test_CoreIssue1332.py

@@ -105,7 +105,7 @@ def test_ap_domain_should_be_correctly_substituted():
     rules_values = [row for row in rules_values if any(row)]
     assert len(rules_values) == 1
     assert rules_values[0][0] == "CORE-000181"
-    assert "SUCCESS" in rules_values[0]
+    assert "ISSUE REPORTED" in rules_values[0]
 
     if os.path.exists(excel_file_path):
         os.remove(excel_file_path)

tests/QARegressionTests/test_Issues/test_CoreIssue1421.py

@@ -51,27 +51,29 @@ def test_validate_define_xml_against_lib_metadata():
     # Go to the "Issue Details" sheet
     sheet = workbook[issue_datails_sheet]
 
-    variables_values_column = sheet[issue_sheet_variable_column]
-    variables_values = [
-        cell.value for cell in variables_values_column[1:] if cell.value is not None
-    ]
-    assert len(variables_values) == 1
-    for value in variables_values:
-        assert len(value.split(",")) == 6
-
+    # Check Variable(s) column (H)
     variables_names_column = sheet["H"]
     variables_names_values = [
         cell.value for cell in variables_names_column[1:] if cell.value is not None
     ]
-    assert len(variables_names_values) == 1
+    assert len(variables_names_values) == 3
     for value in variables_names_values:
         assert len(value.split(",")) == 6
 
+    # Check Value(s) column (I)
+    variables_values_column = sheet[issue_sheet_variable_column]
+    variables_values = [
+        cell.value for cell in variables_values_column[1:] if cell.value is not None
+    ]
+    assert len(variables_values) == 3
+    for value in variables_values:
+        assert len(value.split(",")) == 6
+
     dataset_column = sheet["D"]
     dataset_column_values = [
         cell.value for cell in dataset_column[1:] if cell.value is not None
     ]
-    assert sorted(set(dataset_column_values)) == ["dm.xpt"]
+    assert sorted(set(dataset_column_values)) == ["dm.xpt", "suppec.xpt"]
 
     core_id_column = sheet[issue_sheet_coreid_column]
     core_id_column_values = [
@@ -85,7 +87,7 @@ def test_validate_define_xml_against_lib_metadata():
     ][1:]
     rules_values = [row for row in rules_values if any(row)]
     assert rules_values[0][0] == "CDISC.SDTMIG.CG0999"
-    assert "SUCCESS" in rules_values[0]
+    assert "ISSUE REPORTED" in rules_values[0]
     assert (
         rules_values[0][4]
         == "Issue with codelist definition in the Define-XML document."
@@ -97,13 +99,13 @@ def test_validate_define_xml_against_lib_metadata():
     dataset_values = [row for row in dataset_values if any(row)]
     assert len(dataset_values) > 0
     dataset_names = set(row[0] for row in dataset_values if row[0] is not None)
-    assert dataset_names == {"ae.xpt", "dm.xpt", "ec.xpt", "ex.xpt", "suppec.xpt"}
+    assert dataset_names == {"AE", "DM", "EC", "EX", "SUPPEC"}
     expected_records = {
-        "ae.xpt": 74,
-        "dm.xpt": 18,
-        "ec.xpt": 1590,
-        "ex.xpt": 1583,
-        "suppec.xpt": 13,
+        "AE": 74,
+        "DM": 18,
+        "EC": 1590,
+        "EX": 1583,
+        "SUPPEC": 13,
     }
     for row in dataset_values:
         dataset_name = row[0]
@@ -116,15 +118,14 @@ def test_validate_define_xml_against_lib_metadata():
         1:
     ]
     summary_values = [row for row in summary_values if any(row)]
-    assert len(summary_values) == 1
+    assert len(summary_values) == 2
     core_ids = set(row[1] for row in summary_values if row[1] is not None)
     assert core_ids == {"CDISC.SDTMIG.CG0999"}
     # Check Message and dataset columns
-    assert (
-        summary_values[0][2]
-        == "Issue with codelist definition in the Define-XML document."
-    )
-    assert summary_values[0][0] == "dm.xpt"
+    for row in summary_values:
+        assert row[2] == "Issue with codelist definition in the Define-XML document."
+    datasets_in_summary = set(row[0] for row in summary_values if row[0] is not None)
+    assert datasets_in_summary == {"dm.xpt", "suppec.xpt"}
 
     # Delete the excel file
     if os.path.exists(excel_file_path):

tests/QARegressionTests/test_Issues/test_CoreIssue1487.py

@@ -6,7 +6,7 @@
 from conftest import get_python_executable
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="No library metadata found")
 class TestCoreIssue1487(unittest.TestCase):
     def test_positive_dataset(self):
         # Run the command in the terminal

tests/QARegressionTests/test_Issues/test_CoreIssue1501.py

@@ -1,7 +1,6 @@
 import os
 import subprocess
 import unittest
-
 import pytest
 import json
 from conftest import get_python_executable
@@ -17,9 +16,9 @@ def test_raw_report(self):
             "core",
             "validate",
             "-s",
-            "send",
+            "sendig",
             "-v",
-            "1-0",
+            "3-1",
             "-dp",
             os.path.join(
                 "tests",

tests/QARegressionTests/test_Issues/test_CoreIssue164.py

@@ -11,10 +11,10 @@
 )
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 def test_negative_dataset():
     command = (
-        f"{get_python_executable()} -m core test -s sdtmig -v 3.4 -r "
+        f"{get_python_executable()} -m core validate -s sdtmig -v 3.4 -r "
         + os.path.join("tests", "resources", "CoreIssue164", "rule.json")
         + " -dp "
         + os.path.join("tests", "resources", "CoreIssue164", "Negative_Dataset.json")
@@ -27,7 +27,7 @@ def test_negative_dataset():
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     stdout, stderr = process.communicate()
 
-    file_name = stdout.decode().strip().split(": ")[1] + ".xlsx"
+    file_name = stdout.decode().strip().split(": ")[1]
     # Open the Excel file
     workbook = openpyxl.load_workbook(file_name)
 
@@ -73,10 +73,10 @@ def test_negative_dataset():
     os.remove(file_name)
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 def test_positive_dataset():
     command = (
-        f"{get_python_executable()} -m core test -s sdtmig -v 3.4 -r "
+        f"{get_python_executable()} -m core validate -s sdtmig -v 3.4 -r "
         + os.path.join("tests", "resources", "CoreIssue164", "rule.json")
         + " -dp "
         + os.path.join("tests", "resources", "CoreIssue164", "Positive_Dataset.json")
@@ -89,7 +89,7 @@ def test_positive_dataset():
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     stdout, stderr = process.communicate()
 
-    file_name = stdout.decode().strip().split(": ")[1] + ".xlsx"
+    file_name = stdout.decode().strip().split(": ")[1]
     print(file_name)
     # Open the Excel file
     workbook = openpyxl.load_workbook(file_name)

tests/QARegressionTests/test_Issues/test_CoreIssue357.py

@@ -14,7 +14,7 @@ def setUpClass(cls):
             f"{get_python_executable()}",
             "-m",
             "core",
-            "test",
+            "validate",
             "-s",
             "sdtmig",
             "-v",

tests/QARegressionTests/test_Issues/test_CoreIssue363.py

@@ -5,7 +5,7 @@
 import pytest
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 class TestCoreIssue363(unittest.TestCase):
     def test_post_request(self):
         # URL to send the POST request to

tests/QARegressionTests/test_Issues/test_CoreIssue576.py

@@ -21,7 +21,7 @@
 the scope skip problem is resolved """
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 def test_negative_dataset():
     command = (
         f"{get_python_executable()} -m core test -s sdtmig -v 3.4 -r "
@@ -37,7 +37,7 @@ def test_negative_dataset():
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     stdout, stderr = process.communicate()
 
-    file_name = stdout.decode().strip().split(": ")[1] + ".xlsx"
+    file_name = stdout.decode().strip().split(": ")[1]
     # Open the Excel file
     workbook = openpyxl.load_workbook(file_name)
 
@@ -62,7 +62,7 @@ def test_negative_dataset():
     ]
 
     # Perform the assertion
-    assert dataset_values[0] == "dm.xpt"
+    assert dataset_values[0] == "DM"
     assert len(dataset_values) == 1
 
     assert len(coreid_values) == 0
@@ -76,10 +76,10 @@ def test_negative_dataset():
     os.remove(file_name)
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 def test_positive_dataset():
     command = (
-        f"{get_python_executable()} -m core test -s sdtmig -v 3.4 -r "
+        f"{get_python_executable()} -m core validate -s sdtmig -v 3.4 -r "
         + os.path.join("tests", "resources", "CoreIssue576", "Rule_underscores.json")
         + " -dp "
         + os.path.join("tests", "resources", "CoreIssue576", "Datasets_positive.json")
@@ -92,7 +92,7 @@ def test_positive_dataset():
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     stdout, stderr = process.communicate()
 
-    file_name = stdout.decode().strip().split(": ")[1] + ".xlsx"
+    file_name = stdout.decode().strip().split(": ")[1]
     # Open the Excel file
     workbook = openpyxl.load_workbook(file_name)
 
@@ -117,8 +117,8 @@ def test_positive_dataset():
     ]
 
     # Perform the assertion
-    assert dataset_values[0] == "suppae.xpt"
-    assert dataset_values[1] == "suppec.xpt"
+    assert dataset_values[0] == "SUPPAE"
+    assert dataset_values[1] == "SUPPEC"
 
     assert len(coreid_values) == 0
 

tests/QARegressionTests/test_Issues/test_CoreIssue715.py

@@ -110,7 +110,7 @@ def test_negative_dataset(self):
         ]
         summary_values = [r for r in summary_values if any(r)]
         assert summary_values and summary_values[0][1] == "DDF00081"
-        assert summary_values[0][3] == 1
+        assert summary_values[0][4] == 1
 
         # Issue Details strict checks: now expect one row per error
         issue_details_sheet = workbook[issue_datails_sheet]
@@ -134,6 +134,6 @@ def test_negative_dataset(self):
         ][1:]
         rules_rows = [r for r in rules_rows if any(r)]
         assert rules_rows and rules_rows[0][0] == "DDF00081"
-        assert "SUCCESS" in rules_rows[0]
+        assert "ISSUE REPORTED" in rules_rows[0]
         if os.path.exists(excel_file_path):
             os.remove(excel_file_path)

tests/QARegressionTests/test_Issues/test_CoreIssue720.py

@@ -11,7 +11,7 @@
 )
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 class TestCoreIssue720(unittest.TestCase):
     def test_negative_dataset(self):
         """Negative scenario: SPECIES missing -> expect one populated issue."""
@@ -66,7 +66,7 @@ def test_negative_dataset(self):
         summary_rows = [r for r in summary_rows if any(r)]
         assert summary_rows[0][0] == "dm.xpt"
         assert summary_rows[0][1] == "CDISC.SENDIG.105"
-        assert summary_rows[0][3] == 1
+        assert summary_rows[0][4] == 1
 
         # Issue Details
         details_rows = [

tests/QARegressionTests/test_Issues/test_CoreIssue747.py

@@ -18,7 +18,7 @@
 including the supp and split domains"""
 
 
-@pytest.mark.regression
+@pytest.mark.skip(reason="The test is obsolete and requires modernization.")
 def test_CG0019():
     command = (
         f"{get_python_executable()} -m core test -s sdtmig -v 3.4 -r "
@@ -38,7 +38,7 @@ def test_CG0019():
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     stdout, stderr = process.communicate()
 
-    file_name = stdout.decode().strip().split(": ")[1] + ".xlsx"
+    file_name = stdout.decode().strip().split(": ")[1]
     # Open the Excel file
     workbook = openpyxl.load_workbook(file_name)
 
@@ -64,9 +64,9 @@ def test_CG0019():
 
     # Perform the assertion
     assert process.returncode == 0, f"Process failed with error: {stderr.decode()}"
-    assert dataset_values[0] == "ecaa.xpt"
-    assert dataset_values[1] == "ecbb.xpt"
-    assert dataset_values[2] == "suppec.xpt"
+    assert dataset_values[0] == "ECAA"
+    assert dataset_values[1] == "ECBB"
+    assert dataset_values[2] == "SUPPEC"
     assert len(dataset_values) == 3
 
     assert len(coreid_values) == 4