Define xml

.github/scripts/run_validation.sh

@@ -33,7 +33,7 @@ fi
 echo "Rule file: $RULE_YML"
 
 # ---------------------------------------------------------------------------
-# Initialise report
+# Initialize report
 # ---------------------------------------------------------------------------
 {
   echo "# Rule Validation Report"

Published/CORE-000929/negative/01/data/.env

@@ -1,4 +1,3 @@
 PRODUCT=SDTMIG
 VERSION=3-3
-CT=sdtmct2020-12-18
 DEFINE_XML=define_negative1.xml

Published/CORE-000929/negative/01/results/results.csv

@@ -1,6 +1,5 @@
 Dataset,Record,Variable,Value
-zb.csv,,,
-fa.csv,2,$domain_lib_ccode,"['C49563', 'C49562', 'C117755', 'C147168', 'C147169', 'C147170', 'C132354', 'C147171', 'C147172', 'C147173', 'C147174', 'C147175', 'C147176', 'C147177', 'C147178', 'C147179', 'C111282', 'C111138', 'C111137', 'C85441', 'C49568', 'C49569', 'C102605', 'C49578', 'C95087', 'C102616', 'C102618', 'C49572', 'C102619', 'C102620', 'C49576', 'C102621', 'C102622', 'C49585', 'C102617', 'C117466', 'C102630', 'C49626', 'C49587', 'C85442', 'C117756', 'C102640', 'C102641', 'C117757', 'C61536', 'C102651', 'C112320', 'C49592', 'C49602', 'C49603', 'C95095', 'C102674', 'C49604', 'C102671', 'C61531', 'C102677', 'C147180', 'C161329', 'C106552', 'C49606', 'C49608', 'C111289', 'C61529', 'C147181', 'C49607', 'C102700', 'C49609', 'C95098', 'C147182', 'C147183', 'C102707', 'C107097', 'C106571', 'C49610', 'C49616', 'C147184', 'C112420', 'C117655', 'C49615', 'C147185', 'C147186', 'C147187', 'C147189', 'C147191', 'C147193', 'C147195', 'C147196', 'C147197', 'C147198', 'C147200', 'C147201', 'C147203', 'C147204', 'C147205', 'C147206', 'C147207', 'C147208', 'C147209', 'C147210', 'C147211', 'C147212', 'C147216', 'C147218', 'C147219', 'C147220', 'C147222', 'C147223', 'C147224', 'C147225', 'C147226', 'C165871', 'C147227', 'C147228', 'C147229', 'C147232', 'C147233', 'C147234', 'C147235', 'C147236', 'C147238', 'C147239', 'C147240', 'C147241', 'C147242', 'C147243', 'C147244', 'C147245', 'C147246', 'C147249', 'C147250', 'C147251', 'C147252', 'C147261', 'C147264', 'C147267', 'C147268', 'C147269', 'C49617', 'C49618', 'C117699', 'C49619', 'C49620', 'C147270', 'C106578', 'C53483', 'C106577', 'C49621', 'C95103', 'C102726', 'C49622']"
-fa.csv,2,define_variable_codelist_coded_codes,['C00002']
-vs.csv,2,$domain_lib_ccode,"['C49563', 'C49562', 'C117755', 'C147168', 'C147169', 'C147170', 'C132354', 'C147171', 'C147172', 'C147173', 'C147174', 'C147175', 'C147176', 'C147177', 'C147178', 'C147179', 'C111282', 'C111138', 'C111137', 'C85441', 'C49568', 'C49569', 'C102605', 'C49578', 'C95087', 'C102616', 'C102618', 'C49572', 'C102619', 'C102620', 'C49576', 'C102621', 'C102622', 'C49585', 'C102617', 'C117466', 'C102630', 'C49626', 'C49587', 'C85442', 'C117756', 'C102640', 'C102641', 'C117757', 'C61536', 'C102651', 'C112320', 'C49592', 'C49602', 'C49603', 'C95095', 'C102674', 'C49604', 'C102671', 'C61531', 'C102677', 'C147180', 'C161329', 'C106552', 'C49606', 'C49608', 'C111289', 'C61529', 'C147181', 'C49607', 'C102700', 'C49609', 'C95098', 'C147182', 'C147183', 'C102707', 'C107097', 'C106571', 'C49610', 'C49616', 'C147184', 'C112420', 'C117655', 'C49615', 'C147185', 'C147186', 'C147187', 'C147189', 'C147191', 'C147193', 'C147195', 'C147196', 'C147197', 'C147198', 'C147200', 'C147201', 'C147203', 'C147204', 'C147205', 'C147206', 'C147207', 'C147208', 'C147209', 'C147210', 'C147211', 'C147212', 'C147216', 'C147218', 'C147219', 'C147220', 'C147222', 'C147223', 'C147224', 'C147225', 'C147226', 'C165871', 'C147227', 'C147228', 'C147229', 'C147232', 'C147233', 'C147234', 'C147235', 'C147236', 'C147238', 'C147239', 'C147240', 'C147241', 'C147242', 'C147243', 'C147244', 'C147245', 'C147246', 'C147249', 'C147250', 'C147251', 'C147252', 'C147261', 'C147264', 'C147267', 'C147268', 'C147269', 'C49617', 'C49618', 'C117699', 'C49619', 'C49620', 'C147270', 'C106578', 'C53483', 'C106577', 'C49621', 'C95103', 'C102726', 'C49622']"
-vs.csv,2,define_variable_codelist_coded_codes,['C00004']
+FA,2,$domain_lib_ccode,"['C49563', 'C49562', 'C117755', 'C147168', 'C147169', 'C147170', 'C132354', 'C147171', 'C147172', 'C147173', 'C147174', 'C147175', 'C147176', 'C147177', 'C147178', 'C147179', 'C111282', 'C111138', 'C111137', 'C85441', 'C49568', 'C49569', 'C102605', 'C49578', 'C95087', 'C102616', 'C102618', 'C49572', 'C102619', 'C102620', 'C49576', 'C102621', 'C102622', 'C49585', 'C102617', 'C117466', 'C102630', 'C49626', 'C49587', 'C85442', 'C117756', 'C102640', 'C102641', 'C117757', 'C61536', 'C102651', 'C112320', 'C49592', 'C49602', 'C49603', 'C95095', 'C102674', 'C49604', 'C102671', 'C61531', 'C102677', 'C147180', 'C161329', 'C106552', 'C49606', 'C49608', 'C111289', 'C61529', 'C147181', 'C49607', 'C102700', 'C49609', 'C95098', 'C147182', 'C147183', 'C102707', 'C107097', 'C106571', 'C49610', 'C49616', 'C147184', 'C112420', 'C117655', 'C49615', 'C147185', 'C147186', 'C147187', 'C147189', 'C147191', 'C147193', 'C147195', 'C147196', 'C147197', 'C147198', 'C147200', 'C147201', 'C147203', 'C147204', 'C147205', 'C147206', 'C147207', 'C147208', 'C147209', 'C147210', 'C147211', 'C147212', 'C147216', 'C147218', 'C147219', 'C147220', 'C147222', 'C147223', 'C147224', 'C147225', 'C147226', 'C165871', 'C147227', 'C147228', 'C147229', 'C147232', 'C147233', 'C147234', 'C147235', 'C147236', 'C147238', 'C147239', 'C147240', 'C147241', 'C147242', 'C147243', 'C147244', 'C147245', 'C147246', 'C147249', 'C147250', 'C147251', 'C147252', 'C147261', 'C147264', 'C147267', 'C147268', 'C147269', 'C49617', 'C49618', 'C117699', 'C49619', 'C49620', 'C147270', 'C106578', 'C53483', 'C106577', 'C49621', 'C95103', 'C102726', 'C49622']"
+FA,2,define_variable_codelist_coded_codes,['C00002']
+VS,2,$domain_lib_ccode,"['C49563', 'C49562', 'C117755', 'C147168', 'C147169', 'C147170', 'C132354', 'C147171', 'C147172', 'C147173', 'C147174', 'C147175', 'C147176', 'C147177', 'C147178', 'C147179', 'C111282', 'C111138', 'C111137', 'C85441', 'C49568', 'C49569', 'C102605', 'C49578', 'C95087', 'C102616', 'C102618', 'C49572', 'C102619', 'C102620', 'C49576', 'C102621', 'C102622', 'C49585', 'C102617', 'C117466', 'C102630', 'C49626', 'C49587', 'C85442', 'C117756', 'C102640', 'C102641', 'C117757', 'C61536', 'C102651', 'C112320', 'C49592', 'C49602', 'C49603', 'C95095', 'C102674', 'C49604', 'C102671', 'C61531', 'C102677', 'C147180', 'C161329', 'C106552', 'C49606', 'C49608', 'C111289', 'C61529', 'C147181', 'C49607', 'C102700', 'C49609', 'C95098', 'C147182', 'C147183', 'C102707', 'C107097', 'C106571', 'C49610', 'C49616', 'C147184', 'C112420', 'C117655', 'C49615', 'C147185', 'C147186', 'C147187', 'C147189', 'C147191', 'C147193', 'C147195', 'C147196', 'C147197', 'C147198', 'C147200', 'C147201', 'C147203', 'C147204', 'C147205', 'C147206', 'C147207', 'C147208', 'C147209', 'C147210', 'C147211', 'C147212', 'C147216', 'C147218', 'C147219', 'C147220', 'C147222', 'C147223', 'C147224', 'C147225', 'C147226', 'C165871', 'C147227', 'C147228', 'C147229', 'C147232', 'C147233', 'C147234', 'C147235', 'C147236', 'C147238', 'C147239', 'C147240', 'C147241', 'C147242', 'C147243', 'C147244', 'C147245', 'C147246', 'C147249', 'C147250', 'C147251', 'C147252', 'C147261', 'C147264', 'C147267', 'C147268', 'C147269', 'C49617', 'C49618', 'C117699', 'C49619', 'C49620', 'C147270', 'C106578', 'C53483', 'C106577', 'C49621', 'C95103', 'C102726', 'C49622']"
+VS,2,define_variable_codelist_coded_codes,['C00004']

Published/CORE-000929/negative/02/data/.env

@@ -1,4 +1,3 @@
 PRODUCT=SDTMIG
 VERSION=3-4
-CT=sdtmct2020-12-18
 DEFINE_XML=define_negative2.xml

Published/CORE-000929/positive/01/data/.env

@@ -1,4 +1,3 @@
 PRODUCT=SDTMIG
 VERSION=3-3
-CT=sdtmct2020-12-18
 DEFINE_XML=define_positive1.xml

README.md

@@ -152,7 +152,7 @@ Unpublished/
    **`.env`**
 
    Specifies the standard and version to validate against. `PRODUCT` and `VERSION` are required; `SUBSTANDARD`, `USE_CASE`, `CT`, and `DEFINE_XML` are optional depending on the rule.
-
+   See [`.env.example`](./engine/.env.example) for example env environment variables.
    ```
    PRODUCT=TIG
    VERSION=1-0
@@ -179,14 +179,14 @@ Unpublished/
 
    ```
    dataset,variable,label,type,length
-   cm,STUDYID,Study Identifier,Char,50
-   cm,DOMAIN,Domain Abbreviation,Char,50
-   cm,USUBJID,Unique Subject Identifier,Char,50
-   cm,CMTRT,"Reported Name of Drug, Med, or Therapy",Char,50
-   dm,STUDYID,Study Identifier,Char,50
-   dm,DOMAIN,Domain Abbreviation,Char,50
-   dm,USUBJID,Unique Subject Identifier,Char,50
-   dm,AGE,Age,Num,8
+   CM,STUDYID,Study Identifier,Char,50
+   CM,DOMAIN,Domain Abbreviation,Char,50
+   CM,USUBJID,Unique Subject Identifier,Char,50
+   CM,CMTRT,"Reported Name of Drug, Med, or Therapy",Char,50
+   DM,STUDYID,Study Identifier,Char,50
+   DM,DOMAIN,Domain Abbreviation,Char,50
+   DM,USUBJID,Unique Subject Identifier,Char,50
+   DM,AGE,Age,Num,8
    ...
    ```
 

test.py

@@ -5,6 +5,7 @@
 and writes results.json into each case's results/ directory.
 """
 
+import os
 import sys
 import subprocess
 from pathlib import Path
@@ -13,6 +14,8 @@
 ENGINE_DIR = Path("engine")
 CONVERT_SCRIPT = Path(".github/scripts/convert_results.py")
 
+LOG_LEVELS = ["info", "debug", "error", "critical", "disabled", "warn"]
+
 # ---------------------------------------------------------------------------
 # Rule folder helpers
 # ---------------------------------------------------------------------------
@@ -83,7 +86,13 @@ def next_results_path(results_dir: Path) -> Path:
 # Engine invocation
 # ---------------------------------------------------------------------------
 
-def run_engine(rule_yml: Path, data_dir: Path, output_path: Path) -> tuple[bool, str]:
+def run_engine(
+    rule_yml: Path,
+    data_dir: Path,
+    output_path: Path,
+    log_level: str,
+    capture_logs: bool,
+) -> tuple[bool, str]:
     env_file = find_env_file(data_dir)
     if env_file is None:
         return False, f"No .env file found in {data_dir}"
@@ -96,11 +105,36 @@ def run_engine(rule_yml: Path, data_dir: Path, output_path: Path) -> tuple[bool,
         "-of",  "JSON",
         "-o",   str(output_path.resolve()),
         "-p",   "disabled",
+        "-l",   log_level,
     ]
 
     try:
-        proc = subprocess.run(cmd, cwd=ENGINE_DIR, capture_output=True, text=True)
-        output = (proc.stdout + proc.stderr).strip()
+        env = os.environ.copy()
+
+        stream_output = log_level != "disabled"
+        lines: list[str] = []
+        with subprocess.Popen(
+            cmd,
+            cwd=ENGINE_DIR,
+            env=env,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+            text=True,
+            bufsize=1,
+        ) as proc:
+            for line in proc.stdout:
+                if stream_output:
+                    print(f"    {line}", end="")
+                lines.append(line)
+            proc.wait()
+
+        output = "".join(lines).strip()
+
+        if capture_logs and output:
+            log_path = output_path.parent / f"{output_path.name}_engine.log.txt"
+            log_path.write_text(output, encoding="utf-8")
+            print(f"    Log captured — {log_path}")
+
         return proc.returncode == 0, output
     except Exception as e:
         return False, str(e)
@@ -111,7 +145,12 @@ def run_engine(rule_yml: Path, data_dir: Path, output_path: Path) -> tuple[bool,
 # ---------------------------------------------------------------------------
 
 
-def run_rule(rule_path: Path, specific_case: Optional[str] = None):
+def run_rule(
+    rule_path: Path,
+    specific_case: Optional[str],
+    log_level: str,
+    capture_logs: bool,
+):
     rule_yml  = find_rule_yml(rule_path)
     all_cases = get_test_cases(rule_path)
 
@@ -134,7 +173,7 @@ def run_rule(rule_path: Path, specific_case: Optional[str] = None):
             output_path = next_results_path(case["results_dir"])
 
             print(f"\n  Running {test_type}/{case_id}...")
-            ok, output = run_engine(rule_yml, data_dir, output_path)
+            ok, output = run_engine(rule_yml, data_dir, output_path, log_level, capture_logs)
 
             json_path = Path(str(output_path) + ".json")
             if ok and json_path.exists():
@@ -212,20 +251,42 @@ def prompt_case(cases: Dict[str, List[dict]]) -> Optional[str]:
         print("Invalid — try again.")
 
 
+def prompt_log_level() -> str:
+    print("\nLog level options:")
+    for i, level in enumerate(LOG_LEVELS, 1):
+        print(f"  {i}. {level}")
+    while True:
+        choice = input("Select log level (default: disabled): ").strip().lower()
+        if not choice:
+            return "disabled"
+        if choice in LOG_LEVELS:
+            return choice
+        if choice.isdigit() and 1 <= int(choice) <= len(LOG_LEVELS):
+            return LOG_LEVELS[int(choice) - 1]
+        print("Invalid — try again.")
+
+
+def prompt_capture_logs() -> bool:
+    choice = input("Capture engine logs to results folder? (y/N): ").strip().lower()
+    return choice == "y"
+
+
 # ---------------------------------------------------------------------------
 # Entry point
 # ---------------------------------------------------------------------------
 
 def main():
-    rule_path = prompt_rule_path()
-    cases     = get_test_cases(rule_path)
-    specific  = prompt_case(cases)
-    run_rule(rule_path, specific)
+    rule_path   = prompt_rule_path()
+    cases       = get_test_cases(rule_path)
+    specific    = prompt_case(cases)
+    log_level   = prompt_log_level()
+    capture_logs = prompt_capture_logs()
+    run_rule(rule_path, specific, log_level, capture_logs)
 
 
 if __name__ == "__main__":
     try:
         main()
     except KeyboardInterrupt:
         print("\nInterrupted.")
-        sys.exit(1)
+        sys.exit(1)