1501: fix JSON format report creation when -rr flag is provided

cdisc_rules_engine/services/reporting/json_report.py

@@ -58,7 +58,8 @@ def get_export(
                 json_export[self._get_property_name(sheet_name)] = data_sheet
         if raw_report:
             json_export["results_data"] = [
-                rule_result.to_representation() for rule_result in self._results
+                rule_result.to_representation()
+                for rule_result in self._report_standard._results
             ]
         return json_export
 

tests/QARegressionTests/test_Issues/test_CoreIssue1501.py

@@ -0,0 +1,63 @@
+import os
+import subprocess
+import unittest
+
+import pytest
+import json
+from conftest import get_python_executable
+
+
+@pytest.mark.regression
+class TestCoreIssue1501(unittest.TestCase):
+    def test_raw_report(self):
+        # Run the command in the terminal
+        command = [
+            f"{get_python_executable()}",
+            "-m",
+            "core",
+            "validate",
+            "-s",
+            "send",
+            "-v",
+            "1-0",
+            "-dp",
+            os.path.join(
+                "tests",
+                "resources",
+                "CoreIssue1501",
+                "unit-test-coreid-SENDIG282-negative.json",
+            ),
+            "-lr",
+            os.path.join("tests", "resources", "CoreIssue1501", "Rule.yml"),
+            "-ps",
+            "1",
+            "-of",
+            "json",
+            "-rr",
+        ]
+        subprocess.run(command, check=True)
+
+        # Get the latest created Excel file
+        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))
+        assert {
+            "Conformance_Details",
+            "Dataset_Details",
+            "Issue_Summary",
+            "Issue_Details",
+            "Rules_Report",
+        }.issubset(json_report.keys())
+
+        if "results_data" not in json_report.keys():
+            assert (
+                False
+            ), "'results_data' key not found in report. Expected while using -rr, --raw_report flag"
+        if os.path.exists(json_report_path):
+            os.remove(json_report_path)

tests/resources/CoreIssue1501/Rule.yml

@@ -0,0 +1,132 @@
+Authorities:
+  - Organization: CDISC
+    Standards:
+      - Name: SENDIG
+        References:
+          - Citations:
+              - Cited Guidance:
+                  "Defines the type of specimen used for a measurement. Examples:
+                  SERUM, PLASMA, URINE. If multiple specimen types are used for
+                  a calculation (e.g., serum and urine for creatinine
+                  clearance), then refer to Section 4.3.6.2 for guidance on how
+                  to populate."
+                Document: IG v3.1
+                Item: PPSPEC CDISC Notes
+                Section: 6.3.12
+            Origin: SEND Conformance Rules
+            Rule Identifier:
+              Id: "SEND282"
+              Version: "1"
+            Version: "5.0"
+        Version: "3.1"
+      - Name: SENDIG
+        References:
+          - Citations:
+              - Cited Guidance:
+                  "Defines the type of specimen used for a measurement. Examples:
+                  SERUM, PLASMA, URINE. If multiple specimen types are used for
+                  a calculation (e.g., serum and urine for creatinine
+                  clearance), then refer to Section 4.3.6.2 for guidance on how
+                  to populate."
+                Document: IG v3.1.1
+                Item: PPSPEC CDISC Notes
+                Section: 6.3.12
+            Origin: SEND Conformance Rules
+            Rule Identifier:
+              Id: "SEND282"
+              Version: "1"
+            Version: "5.0"
+        Version: "3.1.1"
+      - Name: SENDIG-DART
+        References:
+          - Citations:
+              - Cited Guidance:
+                  "Defines the type of specimen used for a measurement. Examples:
+                  SERUM, PLASMA, URINE. If multiple specimen types are used for
+                  a calculation (e.g., serum and urine for creatinine
+                  clearance), then refer to Section 4.3.6.2 for guidance on how
+                  to populate."
+                Document: IG v3.1
+                Item: PPSPEC CDISC Notes
+                Section: 6.3.12
+            Origin: SEND Conformance Rules
+            Rule Identifier:
+              Id: "SEND282"
+              Version: "1"
+            Version: "5.0"
+        Version: "1.1"
+      - Name: SENDIG-DART
+        References:
+          - Citations:
+              - Cited Guidance:
+                  "Defines the type of specimen used for a measurement. Examples:
+                  SERUM, PLASMA, URINE. If multiple specimen types are used for
+                  a calculation (e.g., serum and urine for creatinine
+                  clearance), then refer to Section 4.3.6.2 for guidance on how
+                  to populate."
+                Document: IG v3.1.1
+                Item: PPSPEC CDISC Notes
+                Section: 6.3.12
+            Origin: SEND Conformance Rules
+            Rule Identifier:
+              Id: "SEND282"
+              Version: "1"
+            Version: "5.0"
+        Version: "1.2"
+      - Name: SENDIG-GENETOX
+        References:
+          - Citations:
+              - Cited Guidance:
+                  "Defines the type of specimen used for a measurement. Examples:
+                  SERUM, PLASMA, URINE. If multiple specimen types are used for
+                  a calculation (e.g., serum and urine for creatinine
+                  clearance), then refer to Section 4.3.6.2 for guidance on how
+                  to populate."
+                Document: IG v3.1.1
+                Item: PPSPEC CDISC Notes
+                Section: 6.3.12
+            Origin: SEND Conformance Rules
+            Rule Identifier:
+              Id: "SEND282"
+              Version: "1"
+            Version: "5.0"
+        Version: "1.0"
+Check:
+  all:
+    - name: $spec_codelist
+      operator: not_contains_all
+      value: $ppspec_value
+Core:
+  Id: CDISC.SENDIG.SEND282
+  Status: Draft
+  Version: "1"
+Operations:
+  - codelists:
+      - SPEC
+    level: term
+    id: $spec_codelist
+    operator: codelist_terms
+    returntype: value
+  - name: PPSPEC
+    delimiter: ;
+    id: $ppspec_value
+    operator: split_by
+Description: If multiple specimen types are used for a calculation (e.g., serum
+  and urine for creatinine clearance), then this field should be populated with
+  values from the (SPEC) Controlled Terminology codelist delimited by a
+  semicolon.
+Executability: Fully Executable
+Outcome:
+  Message: The multiple specimens are not correctly separated by a semicolon
+  Output Variables:
+    - $ppspec_value
+    - $spec_codelist
+Rule Type: Record Data
+Scope:
+  Classes:
+    Include:
+      - ALL
+  Domains:
+    Include:
+      - ALL
+Sensitivity: Record

tests/resources/CoreIssue1501/unit-test-coreid-SENDIG282-negative.json

@@ -0,0 +1,82 @@
+{
+  "datasets": [
+    {
+      "filename": "pp.xpt",
+      "label": "Pharmacokinetics Parameters",
+      "domain": "PP",
+      "variables": [
+        {
+          "name": "STUDYID",
+          "label": "Study Identifier",
+          "type": "Char",
+          "length": 12
+        },
+        {
+          "name": "DOMAIN",
+          "label": "Domain Abbreviation",
+          "type": "Char",
+          "length": 2
+        },
+        {
+          "name": "USUBJID",
+          "label": "Unique Subject Identifier",
+          "type": "Char",
+          "length": 20
+        },
+        {
+          "name": "PPSEQ",
+          "label": "Sequence Number",
+          "type": "Num",
+          "length": 20
+        },
+        {
+          "name": "PPTESTCD",
+          "label": "Parameter Short Name",
+          "type": "Char",
+          "length": 20
+        },
+        {
+          "name": "PPTEST",
+          "label": "Parameter Name",
+          "type": "Char",
+          "length": 20
+        },
+        {
+          "name": "PPSPEC",
+          "label": "Specimen Material Type",
+          "type": "Char",
+          "length": 20
+        }
+      ],
+      "records": {
+        "STUDYID": [
+          "CDISCPILOT01",
+          "CDISCPILOT01",
+          "CDISCPILOT01",
+          "CDISCPILOT01"
+        ],
+        "DOMAIN": ["PP", "PP", "PP", "PP"],
+        "USUBJID": ["CDISC001", "CDISC001", "CDISC001", "CDISC001"],
+        "PPSEQ": [1, 2, 3, 4],
+        "PPTESTCD": ["TMAX", "TMAX", "TMAX", "TMAX"],
+        "PPTEST": [
+          "Time of CMAX ",
+          "Time of CMAX ",
+          "Time of CMAX ",
+          "Time of CMAX "
+        ],
+        "PPSPEC": [
+          "ABDOMINAL WALL",
+          "ADIPOSE TISSUE, BROWN",
+          "ABDOMINAL WALL|ADIPOSE TISSUE, BROWN",
+          "ABDOMINAL WALL;ADIPOSE TISSUE, BROWN&AIR SAC"
+        ]
+      }
+    }
+  ],
+  "standard": {
+    "product": "sendig",
+    "version": "3-1"
+  },
+  "codelists": []
+}

tests/resources/CoreIssue1501/unit-test-coreid-SENDIG282-positive.json

@@ -0,0 +1,82 @@
+{
+  "datasets": [
+    {
+      "filename": "pp.xpt",
+      "label": "Pharmacokinetics Parameters",
+      "domain": "PP",
+      "variables": [
+        {
+          "name": "STUDYID",
+          "label": "Study Identifier",
+          "type": "Char",
+          "length": 12
+        },
+        {
+          "name": "DOMAIN",
+          "label": "Domain Abbreviation",
+          "type": "Char",
+          "length": 2
+        },
+        {
+          "name": "USUBJID",
+          "label": "Unique Subject Identifier",
+          "type": "Char",
+          "length": 20
+        },
+        {
+          "name": "PPSEQ",
+          "label": "Sequence Number",
+          "type": "Num",
+          "length": 20
+        },
+        {
+          "name": "PPTESTCD",
+          "label": "Parameter Short Name",
+          "type": "Char",
+          "length": 20
+        },
+        {
+          "name": "PPTEST",
+          "label": "Parameter Name",
+          "type": "Char",
+          "length": 20
+        },
+        {
+          "name": "PPSPEC",
+          "label": "Specimen Material Type",
+          "type": "Char",
+          "length": 20
+        }
+      ],
+      "records": {
+        "STUDYID": [
+          "CDISCPILOT01",
+          "CDISCPILOT01",
+          "CDISCPILOT01",
+          "CDISCPILOT01"
+        ],
+        "DOMAIN": ["PP", "PP", "PP", "PP"],
+        "USUBJID": ["CDISC001", "CDISC001", "CDISC001", "CDISC001"],
+        "PPSEQ": [1, 2, 3, 4],
+        "PPTESTCD": ["TMAX", "TMAX", "TMAX", "TMAX"],
+        "PPTEST": [
+          "Time of CMAX ",
+          "Time of CMAX ",
+          "Time of CMAX ",
+          "Time of CMAX "
+        ],
+        "PPSPEC": [
+          "ABDOMINAL WALL",
+          "ADIPOSE TISSUE, BROWN",
+          "ABDOMINAL WALL;ADIPOSE TISSUE, BROWN",
+          "ABDOMINAL WALL;ADIPOSE TISSUE, BROWN;AIR SAC"
+        ]
+      }
+    }
+  ],
+  "standard": {
+    "product": "sendig",
+    "version": "3-1"
+  },
+  "codelists": []
+}