93 lines
3.2 KiB
Python
93 lines
3.2 KiB
Python
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"""Shared local path resolution for the PlantAI/bbav5 runtime."""
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from __future__ import annotations
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import os
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from pathlib import Path
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def _load_local_env(default_root: Path) -> None:
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env_path = default_root / ".env"
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if not env_path.exists():
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return
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for raw_line in env_path.read_text(encoding="utf-8").splitlines():
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line = raw_line.strip()
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if not line or line.startswith("#") or "=" not in line:
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continue
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key, value = line.split("=", 1)
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key = key.strip()
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value = value.strip().strip('"').strip("'")
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if key and key not in os.environ:
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os.environ[key] = value
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def get_project_root() -> Path:
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default_root = Path(__file__).resolve().parents[1]
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_load_local_env(default_root)
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configured = os.environ.get("PLANTAI_PROJECT_ROOT") or os.environ.get("BBAV5_PROJECT_ROOT")
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if configured:
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return Path(configured).expanduser().resolve()
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return default_root
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def get_conda_base() -> Path:
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configured = os.environ.get("BBAV5_CONDA_BASE") or os.environ.get("CONDA_BASE")
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if configured:
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return Path(configured).expanduser().resolve()
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prefix = Path(os.environ.get("CONDA_PREFIX", os.path.expanduser("~/miniconda3"))).expanduser().resolve()
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return prefix.parent.parent if prefix.parent.name == "envs" else prefix
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def get_conda_env_bin(env_name: str) -> Path:
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"""Return the bin directory for a conda environment, e.g. get_conda_env_bin('test4py311') -> /path/to/miniconda3/envs/test4py311/bin"""
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return get_conda_base() / "envs" / env_name / "bin"
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def get_conda_env_python(env_name: str) -> Path:
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"""Return the python executable for a conda environment."""
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return get_conda_env_bin(env_name) / "python"
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def get_conda_env_rscript(env_name: str) -> Path:
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"""Return the Rscript executable for a conda environment."""
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return get_conda_env_bin(env_name) / "Rscript"
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def get_configured_path(name: str, default: str = "") -> str:
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"""Return one deployment path supplied by the loaded project environment."""
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return str(os.environ.get(name) or default).strip()
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def get_wgs_samtools(stage: str, requested: str = "") -> str:
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"""Resolve the stage-authoritative samtools executable."""
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if str(stage or "") == "wgs_bam_qc":
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rnaseq_env = get_configured_path("BBAV5_RNASEQ_ENV", "rnaseq")
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return str(get_conda_env_bin(rnaseq_env) / "samtools")
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return str(requested or (get_conda_env_bin("ASAW") / "samtools"))
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def get_wgs_java(requested: str = "") -> str:
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"""Resolve the Java executable used by Beagle imputation."""
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return str(
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requested
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or get_configured_path("WGS_JAVA")
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or (get_conda_env_bin("test4py311") / "java")
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)
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def get_wgs_bcftools(requested: str = "") -> str:
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"""Resolve the CPU-compatible bcftools executable for WGS stages."""
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return str(
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requested
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or get_configured_path("WGS_BCFTOOLS")
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or (get_conda_env_bin("ASAW") / "bcftools")
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)
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PROJECT_ROOT = get_project_root()
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WORKSPACE_ROOT = PROJECT_ROOT / "workspace"
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INPUT_ROOT = PROJECT_ROOT / "input"
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MEMORY_ROOT = PROJECT_ROOT / "memory_storage"
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PROMPTS_DIR = PROJECT_ROOT / "prompts"
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CONDA_BASE = get_conda_base()
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