#1348 fix not as head condition provides proper AST

cdisc_rules_engine/models/rule_conditions/condition_composite_factory.py

@@ -28,11 +28,16 @@ def get_condition_composite(
                 )
 
             if key == AllowedConditionsKeys.NOT.value:
-                # "not" composite wraps a regular composite
-                return NotConditionComposite(
+                not_inner = cls.get_condition_composite(condition_list)
+                not_composite = NotConditionComposite(
                     key=key,
-                    condition_composite=cls.get_condition_composite(conditions["not"]),
+                    condition_composite=not_inner,
                 )
+                composite.add_conditions(
+                    AllowedConditionsKeys.ALL.value,
+                    [not_composite],
+                )
+                continue
             else:
                 # create a regular composite
                 conditions_to_add = []

tests/QARegressionTests/test_Issues/test_CoreIssue1348.py

@@ -0,0 +1,234 @@
+import os
+import subprocess
+
+import pytest
+import json
+from conftest import get_python_executable
+
+_message = (
+    "The study version's study phase is not specified according to the extensible Trial Phase Response"
+    ' (C66737) SDTM codelist - codeSystem is not "http://www.cdisc.org", codeSystemVersion is not a valid'
+    " terminology package date, and/or the code or decode is found in the codelist (case insensitive)"
+    " but the corresponding decode or code does not match the codelist value (case sensitive)."
+)
+_summary = [
+    {
+        "dataset": "StudyVersion.xpt",
+        "core_id": "CORE-000409",
+        "message": _message,
+        "issues": 7,
+    }
+]
+_issue_details = [
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 1,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": [
+            "C199989",
+            "C199989",
+            "Phase II Trial",
+            "PHASE II TRIAL",
+            "C15601",
+            "Phase Ib Trial",
+        ],
+    },
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 2,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": ["null", "null", "Not Applicable", "NOT APPLICABLE", "C48660", "N/A"],
+    },
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 3,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": [
+            "C198366",
+            "C198366",
+            "null",
+            "null",
+            "C198366xx",
+            "Phase I/II/III Trial",
+        ],
+    },
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 4,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": ["C15600", "C15600", "null", "null", "C00001x", "Phase I Trial"],
+    },
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 5,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": [
+            "C198366",
+            "C198366",
+            "Phase II Trial",
+            "PHASE II TRIAL",
+            "C15601",
+            "Phase I/II/III Trial",
+        ],
+    },
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 6,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": ["C199989", "C199989", "null", "null", "C198366xx", "PHASE IB TRIAL"],
+    },
+    {
+        "core_id": "CORE-000409",
+        "message": _message,
+        "executability": "fully executable",
+        "dataset": "StudyVersion.xpt",
+        "USUBJID": "",
+        "row": 7,
+        "SEQ": "",
+        "variables": [
+            "$code_for_pref_term",
+            "$code_for_value",
+            "$pref_term_for_code",
+            "$value_for_code",
+            "studyPhase.standardCode.code",
+            "studyPhase.standardCode.decode",
+        ],
+        "values": [
+            "null",
+            "null",
+            "Phase Ib Trial",
+            "PHASE IB TRIAL",
+            "C199989",
+            "PHASE 2 TRIAL",
+        ],
+    },
+]
+
+
+@pytest.mark.regression
+class TestCoreIssue1348:
+    @pytest.mark.parametrize(
+        "rule_name, dataset, issue_summary, details",
+        [
+            ("DDF00015_not.yaml", "data_pos", [], []),
+            ("DDF00015_not.yaml", "data_neg", _summary, _issue_details),
+            ("DDF00015_all.yaml", "data_pos", [], []),
+            ("DDF00015_all.yaml", "data_neg", _summary, _issue_details),
+        ],
+    )
+    def test_not_as_first_condition_same_errors_as_all_condition(
+        self, rule_name, dataset, issue_summary, details
+    ):
+        # Run the command in the terminal
+        command = [
+            f"{get_python_executable()}",
+            "-m",
+            "core",
+            "validate",
+            "-s",
+            "sdtmig",
+            "-v",
+            "3-4",
+            "-lr",
+            os.path.join("tests", "resources", "CoreIssue1348", rule_name),
+            "-of",
+            "json",
+            "--data",
+            os.path.join("tests", "resources", "CoreIssue1348", dataset),
+        ]
+        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())
+
+        assert details == json_report["Issue_Details"]
+        assert issue_summary == json_report["Issue_Summary"]
+        if os.path.exists(json_report_path):
+            os.remove(json_report_path)

tests/resources/CoreIssue1348/DDF00015_all.yaml

@@ -0,0 +1,117 @@
+Authorities:
+  - Organization: CDISC
+    Standards:
+      - Name: USDM
+        References:
+          - Citations:
+              - Cited Guidance:
+                  "A study version's study phase must be specified according to
+                  the extensible Trial Phase Response (C66737) SDTM codelist
+                  (e.g. an entry with a code or decode used from the codelist
+                  should be consistent with the full entry in the codelist)."
+                Document: "USDM_CORE_Rules.xlsx"
+            Origin: "USDM Conformance Rules"
+            Rule Identifier:
+              Id: "DDF00015"
+              Version: "1"
+            Version: "1.0"
+        Version: "3.0"
+Check:
+  all:
+    - not:
+        any:
+          - all:
+              - name: $code_for_pref_term
+                operator: empty
+              - name: $code_for_value
+                operator: empty
+              - name: $pref_term_for_code
+                operator: empty
+              - name: $value_for_code
+                operator: empty
+          - all:
+              - name: $pref_term_for_code
+                operator: non_empty
+              - name: $value_for_code
+                operator: non_empty
+              - any:
+                  - name: $code_for_pref_term
+                    operator: non_empty
+                  - name: $code_for_value
+                    operator: non_empty
+              - any:
+                  - name: studyPhase.standardCode.code
+                    operator: equal_to
+                    value: $code_for_pref_term
+                  - name: studyPhase.standardCode.code
+                    operator: equal_to
+                    value: $code_for_value
+              - any:
+                  - name: studyPhase.standardCode.decode
+                    operator: equal_to
+                    value: $pref_term_for_code
+                  - name: studyPhase.standardCode.decode
+                    operator: equal_to
+                    value: $value_for_code
+Core:
+  Id: "CORE-000409"
+  Status: Draft
+  Version: "1"
+Description: "A study version's study phase must be specified according to the
+  extensible Trial Phase Response (C66737) SDTM codelist (e.g. an entry with a
+  code or decode used from the codelist should be consistent with the full entry
+  in the codelist)."
+Executability: Fully Executable
+Operations:
+  - id: $codelist_code
+    map:
+      - output: C66737
+    operator: map
+  - codelist_code: $codelist_code
+    ct_package_type: SDTM
+    id: $value_for_code
+    operator: codelist_terms
+    term_code: studyPhase.standardCode.code
+    version: studyPhase.standardCode.codeSystemVersion
+    returntype: value
+  - codelist_code: $codelist_code
+    ct_package_type: SDTM
+    id: $pref_term_for_code
+    operator: codelist_terms
+    term_code: studyPhase.standardCode.code
+    version: studyPhase.standardCode.codeSystemVersion
+    returntype: pref_term
+  - codelist_code: $codelist_code
+    ct_package_type: SDTM
+    id: $code_for_pref_term
+    operator: codelist_terms
+    term_pref_term: studyPhase.standardCode.decode
+    version: studyPhase.standardCode.codeSystemVersion
+    returntype: code
+  - codelist_code: $codelist_code
+    ct_package_type: SDTM
+    id: $code_for_value
+    operator: codelist_terms
+    term_value: studyPhase.standardCode.decode
+    version: studyPhase.standardCode.codeSystemVersion
+    returntype: code
+Outcome:
+  Message: 'The study version''s study phase is not specified according to the
+    extensible Trial Phase Response (C66737) SDTM codelist - codeSystem is not
+    "http://www.cdisc.org", codeSystemVersion is not a valid terminology package
+    date, and/or the code or decode is found in the codelist (case insensitive)
+    but the corresponding decode or code does not match the codelist value (case
+    sensitive).'
+  Output Variables:
+    - $code_for_pref_term
+    - $code_for_value
+    - $pref_term_for_code
+    - $value_for_code
+    - studyPhase.standardCode.code
+    - studyPhase.standardCode.decode
+Rule Type: Record Data
+Scope:
+  Entities:
+    Include:
+      - "StudyVersion"
+Sensitivity: Record