| |
| """ |
| Annotate runtime environment for Bioconda tool JSON files. |
| |
| Default targets: |
| - output/bioconda_source_tool/bioconda_t0_core_tools.json |
| - output/bioconda_source_tool/bioconda_t1_domain_tools.json |
| - output/bioconda_source_tool/bioconda_t2_on_demand_tools.json |
| """ |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| from pathlib import Path |
| from typing import Dict, List, Tuple |
|
|
|
|
| def _lower_list(values: List[str]) -> List[str]: |
| return [str(v).strip().lower() for v in values if str(v).strip()] |
|
|
|
|
| def infer_runtime(package_name: str, dependencies: List[str], summary: str, description: str) -> Tuple[str, str]: |
| pkg = package_name.lower() |
| deps = _lower_list(dependencies) |
| text = f"{summary} {description}".lower() |
|
|
| |
| if pkg.startswith("r-") or pkg.startswith("bioconductor-"): |
| return "R", "package_name prefix indicates R/Bioconductor ecosystem" |
| if any(d.startswith("r-") or "r-base" in d for d in deps): |
| return "R", "dependencies include r-base or r-* packages" |
|
|
| |
| if pkg.startswith("perl-") or any(d.startswith("perl-") or d == "perl" for d in deps): |
| return "Perl", "package/dependencies indicate Perl runtime" |
|
|
| |
| if any("openjdk" in d or "default-jre" in d or d == "java" for d in deps): |
| return "Java", "dependencies include Java runtime (openjdk/jre)" |
|
|
| |
| if any("python" in d for d in deps): |
| return "Python", "dependencies include python" |
| py_keywords = ("python", "pypi", "scanpy", "scvelo", "scvi", "anndata") |
| if any(k in text for k in py_keywords): |
| return "Python", "summary/description contains Python ecosystem keywords" |
|
|
| |
| compiled_markers = ("libgcc", "libstdcxx", "htslib", "zlib", "gcc", "gxx") |
| if any(any(m in d for m in compiled_markers) for d in deps): |
| return "Compiled", "dependencies suggest compiled/native executable" |
|
|
| return "Other", "no strong signal for Python/R/Perl/Java; marked as Other" |
|
|
|
|
| def annotate_file(json_path: Path, inplace: bool = True) -> Dict[str, int]: |
| if not json_path.exists(): |
| return {"total": 0, "updated": 0} |
|
|
| with json_path.open("r", encoding="utf-8") as f: |
| rows = json.load(f) |
| if not isinstance(rows, list): |
| raise ValueError(f"JSON root must be list: {json_path}") |
|
|
| updated = 0 |
| for row in rows: |
| if not isinstance(row, dict): |
| continue |
| runtime, reason = infer_runtime( |
| package_name=str(row.get("package_name", "")).strip(), |
| dependencies=list(row.get("dependencies", []) or []), |
| summary=str(row.get("summary", "")).strip(), |
| description=str(row.get("description", "")).strip(), |
| ) |
| row["execution_environment"] = runtime |
| row["execution_environment_reason"] = reason |
| updated += 1 |
|
|
| if inplace: |
| with json_path.open("w", encoding="utf-8") as f: |
| json.dump(rows, f, ensure_ascii=False, indent=2) |
|
|
| return {"total": len(rows), "updated": updated} |
|
|
|
|
| def main() -> None: |
| parser = argparse.ArgumentParser(description="Add execution environment annotations to tool JSON files.") |
| parser.add_argument( |
| "--files", |
| nargs="*", |
| default=[ |
| "/225040511/project/BioScientist/agent_system/toolbase/output/bioconda_source_tool/bioconda_t0_core_tools.json", |
| "/225040511/project/BioScientist/agent_system/toolbase/output/bioconda_source_tool/bioconda_t1_domain_tools.json", |
| "/225040511/project/BioScientist/agent_system/toolbase/output/bioconda_source_tool/bioconda_t2_on_demand_tools.json", |
| ], |
| help="Target JSON files.", |
| ) |
| args = parser.parse_args() |
|
|
| results = {} |
| for p in args.files: |
| path = Path(p) |
| stats = annotate_file(path, inplace=True) |
| results[str(path)] = stats |
| print(f"{path}: updated {stats['updated']}/{stats['total']}") |
|
|
| report_path = Path("/225040511/project/BioScientist/agent_system/toolbase/output/bioconda_source_tool/runtime_annotation_report.json") |
| report_path.parent.mkdir(parents=True, exist_ok=True) |
| with report_path.open("w", encoding="utf-8") as f: |
| json.dump(results, f, ensure_ascii=False, indent=2) |
| print(f"Saved report: {report_path}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
