| """Where the app reads its data, in one place and overridable per deployment. |
| |
| Sixteen modules under `src/endopath/` and `scripts/` each computed the checkout root, and fifteen |
| rooted data at a bare `Path("data")` that resolves against the working directory rather than the |
| checkout, so the same call read a different file depending on where the process started. Nothing but |
| the embeddings directory could be pointed elsewhere, so a second registry could not be loaded and a |
| deployment could not separate its data from its code. |
| |
| Every root here reads an environment variable first and falls back to the checkout, so a deployment |
| points the app at its own data without editing source, and a test points it at a fixture directory. |
| |
| Standard library only, so this module sits below every other one in the import graph. Importing it |
| through the package still pulls pydantic, because `endopath/__init__.py` imports `schema`. A script |
| that builds its own environment from a PEP 723 dependency list therefore declares pydantic, as |
| `scripts/scrape_barcodes.py` does. |
| """ |
|
|
| from __future__ import annotations |
|
|
| import os |
| from pathlib import Path |
|
|
| |
| REPO_ROOT = Path(__file__).resolve().parents[2] |
|
|
|
|
| def _rooted(env_var: str, *default: str) -> Path: |
| """The directory `env_var` names, or the checkout-relative default. A relative override resolves |
| against the working directory, so a deployment may pass either shape.""" |
| override = os.environ.get(env_var, "").strip() |
| return Path(override).expanduser().resolve() if override else REPO_ROOT.joinpath(*default) |
|
|
|
|
| |
| DATA_DIR = _rooted("ENDOPATH_DATA_DIR", "data") |
| |
| |
| TAXONOMY_DIR = _rooted("ENDOPATH_TAXONOMY_DIR", "data", "taxonomy") |
| DOCS_DIR = _rooted("ENDOPATH_DOCS_DIR", "docs") |
|
|
| RAW_DIR = DATA_DIR / "raw" |
| IMAGE_DIR = DATA_DIR / "images" |
| INTERIM_DIR = DATA_DIR / "interim" |
| EMBEDDINGS_DIR = _rooted("ENDOPATH_EMBEDDINGS_DIR", "data", "embeddings") |
| METADATA_DIR = DATA_DIR / "tcga_metadata" |
| DEMO_CORPUS_DIR = DATA_DIR / "demo_corpus" |
|
|
| REPORTS_CSV_PATH = RAW_DIR / "TCGA_Reports.csv" |
| PDF_DIR = RAW_DIR / "pdfs" |
| TAXONOMY_DOC_PATH = DOCS_DIR / "taxonomy.md" |
|
|
