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c0a7163 c7e27e5 c0a7163 c7e27e5 c0a7163 c7e27e5 c0a7163 c7e27e5 c0a7163 c7e27e5 c0a7163 c7e27e5 c00e850 c0a7163 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | #!/bin/sh
set -eu
mkdir -p data/raw data/processed data/knowledge_base/seed
# Seed raw fixtures so the Signal/Image/Molecule tabs work on first click.
if [ -f tests/fixtures/bbbp_sample.csv ] && [ ! -f data/raw/bbbp.csv ]; then
cp tests/fixtures/bbbp_sample.csv data/raw/bbbp.csv
fi
if [ -f tests/fixtures/eeg_sample.fif ] && [ ! -f data/raw/eeg.fif ]; then
cp tests/fixtures/eeg_sample.fif data/raw/eeg.fif
fi
if [ -d tests/fixtures/kb_sample ] && [ ! -f data/knowledge_base/seed/lipinski_rule_of_five.md ]; then
cp tests/fixtures/kb_sample/* data/knowledge_base/seed/
fi
# Demo-time stub artifacts (MRI 2D / volumetric ONNX / EEG joblib / clinical
# RAG / axial PNG). Idempotent — only fills missing.
python scripts/seed_demo_artifacts.py || true
# BBB feature extraction + classifier training (idempotent).
if [ ! -f data/processed/bbbp_features.parquet ]; then
NEUROBRIDGE_DISABLE_MLFLOW=1 python -m src.pipelines.bbb_pipeline || true
fi
if [ ! -f data/processed/bbb_model.joblib ]; then
NEUROBRIDGE_DISABLE_MLFLOW=1 python -m src.models.bbb_model || true
fi
# EEG feature extraction (idempotent).
if [ ! -f data/processed/eeg_features.parquet ]; then
NEUROBRIDGE_DISABLE_MLFLOW=1 python -c "
from pathlib import Path
from src.pipelines.eeg_pipeline import run_pipeline
run_pipeline(
input_path=Path('tests/fixtures/eeg_sample.fif'),
output_path=Path('data/processed/eeg_features.parquet'),
)
" || true
fi
# MRI feature extraction + ComBat harmonization (idempotent).
if [ ! -f data/processed/mri_features.parquet ]; then
NEUROBRIDGE_DISABLE_MLFLOW=1 python -c "
from pathlib import Path
from src.pipelines.mri_pipeline import run_pipeline
run_pipeline(
input_dir=Path('tests/fixtures/mri_sample'),
sites_csv=Path('tests/fixtures/mri_sample/sites.csv'),
output_path=Path('data/processed/mri_features.parquet'),
)
" || true
fi
# RAG FAISS index build (idempotent).
if [ ! -f data/processed/faiss_index/index.bin ]; then
python -m src.rag.ingest data/knowledge_base data/processed/faiss_index || true
fi
exec "$@"
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