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Users can now specify the location for SoMEF outputs issue #53 #54

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Merged
Anas-Elhounsri merged 1 commit into from
Mar 5, 2026
Merged

Users can now specify the location for SoMEF outputs issue #53 #54

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3 changes: 2 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,7 @@ The `repositories.json` file should be structured as follows:

```bash
poetry run rsmetacheck --input repositories.json \
--somef-output ./results/somef \
--pitfalls-output ./results/pitfalls \
--analysis-output ./results/summary.json
```
Expand Down Expand Up @@ -127,7 +128,7 @@ poetry run rsmetacheck --input https://github.com/tidyverse/tidyverse --verbose

The tool will:

- Process all JSON files in the `somef_outputs` (by default created by the tool) directory
- Process all JSON files in the SoMEF output directory (by default `somef_outputs` created by the tool)
- Display progress messages showing detected pitfalls
- Generate JSON-LD files of detailed Pitfalls and Warnings detected by the tool in `output_1_pitfalls.jsonld`,
`output_2_pitfalls.jsonld`, etc... in `pitfalls` (by default created by the tool) directory
Expand Down
7 changes: 6 additions & 1 deletion src/metacheck/cli.py
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Expand Up @@ -23,6 +23,11 @@ def cli():
default=os.path.join(os.getcwd(), "pitfalls_outputs"),
help="Directory to store pitfall JSON-LD files (default: ./pitfalls_outputs)."
)
parser.add_argument(
"--somef-output",
default=os.path.join(os.getcwd(), "somef_outputs"),
help="Directory to store SoMEF output files (default: ./somef_outputs)."
)
parser.add_argument(
"--analysis-output",
default=os.path.join(os.getcwd(), "analysis_results.json"),
Expand Down Expand Up @@ -62,7 +67,7 @@ def cli():

else:
threshold = args.threshold
somef_output_dir = os.path.join(os.getcwd(), "somef_outputs")
somef_output_dir = args.somef_output

print(f"Detected {len(args.input)} input(s):")

Expand Down
3 changes: 2 additions & 1 deletion src/metacheck/detect_pitfalls_main.py
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Expand Up @@ -374,7 +374,6 @@ def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[s
except Exception as e:
print(f"Error creating JSON-LD for {json_file.name}: {e}")

# Capture commit ID in evaluated_repositories summary
try:
repo_name = json_file.name
if "full_name" in somef_data and somef_data["full_name"]:
Expand Down Expand Up @@ -413,6 +412,8 @@ def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[s
results["summary"]["total_warnings_detected"] = total_warnings

for i, count in enumerate(pitfall_counts):
pitfall_code_str = pitfall_detectors[i][1]
results["pitfalls & warnings"][i]["pitfall"] = f"https://w3id.org/rsmetacheck/catalog/#{pitfall_code_str}"
results["pitfalls & warnings"][i]["count"] = count
if total_repos > 0:
results["pitfalls & warnings"][i]["percentage"] = round((count / total_repos) * 100, 2)
Expand Down
7 changes: 2 additions & 5 deletions src/metacheck/utils/json_ld_utils.py
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Expand Up @@ -484,7 +484,6 @@ def create_pitfall_jsonld(somef_data: Dict, pitfall_results: List[Dict], file_na
"""
Create a JSON-LD structure for detected pitfalls following the sample format.
"""
import hashlib
software_info = extract_software_info_from_somef(somef_data)
description_info = extract_description_info(somef_data)

Expand Down Expand Up @@ -516,7 +515,7 @@ def create_pitfall_jsonld(somef_data: Dict, pitfall_results: List[Dict], file_na

output_val = "true" if has_issue else "false"
evidence_val = format_evidence_text(pitfall_code, pitfall_result) if has_issue else f"{pitfall_code} not detected:"
suggestion_val = get_suggestion_text(pitfall_code) if has_issue else ""
suggestion_val = get_suggestion_text(pitfall_code) if has_issue else "N/A"

check_result = {
"@type": "CheckResult",
Expand All @@ -529,13 +528,11 @@ def create_pitfall_jsonld(somef_data: Dict, pitfall_results: List[Dict], file_na
},
"process": get_pitfall_description(pitfall_code),
"status": {"@id": "schema:CompletedActionStatus"},
"pitfall": f"https://w3id.org/rsmetacheck/catalog/#{pitfall_code}",
"output": output_val,
"evidence": evidence_val,
"suggestion": suggestion_val
}

check_hash = hashlib.sha256(json.dumps(check_result, sort_keys=True).encode("utf-8")).hexdigest()
check_result["checkId"] = check_hash

jsonld_output["checks"].append(check_result)

Expand Down