diff --git a/cdisc_rules_engine/rules_engine.py b/cdisc_rules_engine/rules_engine.py index 9ff27c034..05bba3b91 100644 --- a/cdisc_rules_engine/rules_engine.py +++ b/cdisc_rules_engine/rules_engine.py @@ -195,9 +195,13 @@ def _update_total_errors_and_check_limit( def _truncate_dataset_errors(self, dataset_results, rule, dataset_metadata): for result in dataset_results: - if result.get("executionStatus") == "success": + if result.get("executionStatus") in [ + ExecutionStatus.ISSUE_REPORTED.value, + ExecutionStatus.SUCCESS.value, + ]: errors = result.get("errors", []) if len(errors) > self.max_errors_per_rule: + result["original_errors_len"] = len(errors) result["errors"] = errors[: self.max_errors_per_rule] logger.info( f"Rule {rule.get('core_id')}: Truncated {len(errors)} errors to " diff --git a/cdisc_rules_engine/services/reporting/sdtm_report_data.py b/cdisc_rules_engine/services/reporting/sdtm_report_data.py index 5ab0d8e7a..4f5180648 100644 --- a/cdisc_rules_engine/services/reporting/sdtm_report_data.py +++ b/cdisc_rules_engine/services/reporting/sdtm_report_data.py @@ -224,11 +224,14 @@ def get_summary_data(self) -> list[dict]: result.get("errors") and result.get("executionStatus") != ExecutionStatus.SKIPPED.value ): + issues = result.get("original_errors_len") or len( + result.get("errors", []) + ) summary_item = { "dataset": dataset, "core_id": validation_result.id, "message": result.get("message"), - "issues": len(result.get("errors")), + "issues": issues, } summary_data.append(summary_item) diff --git a/tests/QARegressionTests/test_Issues/test_CoreIssue1718.py b/tests/QARegressionTests/test_Issues/test_CoreIssue1718.py new file mode 100644 index 000000000..926839bdf --- /dev/null +++ b/tests/QARegressionTests/test_Issues/test_CoreIssue1718.py @@ -0,0 +1,60 @@ +import os +import subprocess +import pytest +import json +from conftest import get_python_executable + + +@pytest.mark.regression +class TestCoreIssue1718: + def test_max_issues(self): + # Run the command in the terminal + max_issues = 3 + command = [ + f"{get_python_executable()}", + "-m", + "core", + "validate", + "-s", + "sdtmig", + "-v", + "3-4", + "-d", + os.path.join( + "tests", + "resources", + "CoreIssue1718", + ), + "-r", + "CORE-000356", + "-ps", + "1", + "-of", + "json", + "-me", + f"{max_issues}", + "true", + ] + 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] + json_report = json.load(open(json_report_path)) + assert { + "Conformance_Details", + "Dataset_Details", + "Issue_Summary", + "Issue_Details", + "Rules_Report", + }.issubset(json_report.keys()) + assert json_report["Rules_Report"][0]["status"] == "ISSUE REPORTED" + assert json_report["Issue_Summary"][0]["issues"] == 74 + assert len(json_report["Issue_Details"]) == max_issues + + if os.path.exists(json_report_path): + os.remove(json_report_path) diff --git a/tests/resources/CoreIssue1718/ae.json b/tests/resources/CoreIssue1718/ae.json new file mode 100644 index 000000000..c249351e5 --- /dev/null +++ b/tests/resources/CoreIssue1718/ae.json @@ -0,0 +1,3163 @@ +{ + "datasetJSONCreationDateTime": "2024-11-11T15:09:14", + "datasetJSONVersion": "1.1.0", + "fileOID": "www.cdisc.org/StudyMSGv2/1/Define-XML_2.1.0/2024-11-11/ae", + "dbLastModifiedDateTime": "2020-08-21T09:14:28", + "originator": "CDISC SDTM MSG Team", + "sourceSystem": { "name": "SAS on X64_10PRO", "version": "9.0401M7" }, + "studyOID": "cdisc.com/CDISCPILOT01", + "metaDataVersionOID": "MDV.MSGv2.0.SDTMIG.3.3.SDTM.1.7", + "metaDataRef": "define.xml", + "itemGroupOID": "IG.AE", + "records": 74, + "name": "AE", + "label": "Adverse Events", + "columns": [ + { + "itemOID": "IT.AE.STUDYID", + "name": "STUDYID", + "label": "Study Identifier", + "dataType": "string", + "length": 12, + "keySequence": 1 + }, + { + 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