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Add analysis/replicate.sh — single-command driver for the primary analysis #1

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166 changes: 166 additions & 0 deletions analysis/replicate.sh
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#!/usr/bin/env bash
# replicate.sh — single-command end-to-end replication of the *primary*
# analysis (the one reported in the original submission). This is kept
# separate from revisions/replicate.sh, which drives the revision-round
# pipeline. Run from the repository root.
#
# Usage:
# ./analysis/replicate.sh # run everything
# DRY_RUN=1 ./analysis/replicate.sh # print commands without running
# PHASES="downloads,strains" ./analysis/replicate.sh # run a subset
#
# Phases (in execution order):
# keys Verify the OpenAI API key is reachable (Keychain → env
# → ~/openai/access_key.txt fallback used by inst/gpt.py)
# downloads Shared ontology / jar downloads required by both tasks
# (analysis/_downloads/download.R)
# strains Strain-task pipeline:
# 00 download Gemma annotations + build strain dictionary
# 01 regex baseline
# 02 GPT-4o annotation (OpenAI Batch — can take hours)
# 03 evaluate predictions vs curator
# 04 post-curation cleanup
# cells Cell-line pipeline:
# 00 download Gemma annotations + embed cell-line terms
# 01 process cell-line dictionary
# 02 GPT-4o first-pass annotation (OpenAI Batch)
# 03 compare extractions to vector index
# 04 build RAG inputs
# 05 GPT-4o RAG resolution pass (OpenAI Batch)
# 06 evaluate predictions vs curator
# 07 post-curator evaluation
#
# Scripts 02 / 05 submit OpenAI Batch jobs. They block internally on
# batch completion via R/run_batches.R, so the bash driver does not
# need a poll loop of its own — the underlying R loop already handles
# resume-on-restart. Each batch can take up to 24 hours; typical
# turnaround is much faster.

set -euo pipefail
shopt -s expand_aliases

# ---------------------------------------------------------------------------
# Locations
# ---------------------------------------------------------------------------
REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")"/.. && pwd)"
cd "$REPO_ROOT"
ANA="$REPO_ROOT/analysis"
RSCRIPT="${RSCRIPT:-Rscript}"

PHASES="${PHASES:-keys,downloads,strains,cells}"

# ---------------------------------------------------------------------------
# DRY_RUN: print + skip; otherwise execute
# ---------------------------------------------------------------------------
run() {
if [[ "${DRY_RUN:-0}" == "1" ]]; then
printf " [dry-run] %s\n" "$*"
else
printf " [run] %s\n" "$*"
eval "$@"
fi
}

phase() {
local name="$1"; shift
if [[ ",$PHASES," == *",$name,"* ]]; then
echo
echo "============================================================"
echo "PHASE: $name"
echo "============================================================"
"$@"
else
printf "(skipping phase: %s)\n" "$name"
fi
}

# ---------------------------------------------------------------------------
# Keychain helper (per ~/.claude/CLAUDE.md): resolve a credential from the
# macOS Keychain into an environment variable, trying several plausible
# service names. Honours pre-set env vars so manual overrides still work.
# ---------------------------------------------------------------------------
keychain_export() {
local var="$1"; shift
if [[ -n "${!var:-}" ]]; then
return 0
fi
local val=""
for entry in "$@"; do
[ -z "$entry" ] && continue
if val=$(security find-generic-password -s "$entry" -w 2>/dev/null); then
export "$var=$val"
return 0
fi
done
return 1
}

# ---------------------------------------------------------------------------
# keys: ensure the OpenAI key is reachable. inst/gpt.py reads (in order)
# ~/openai/access_key.txt, then OPENAI_API_KEY env. We resolve from
# Keychain into OPENAI_API_KEY when neither is already set.
# ---------------------------------------------------------------------------
verify_keys() {
if [[ "${DRY_RUN:-0}" == "1" ]]; then
printf " [dry-run] resolve OPENAI_API_KEY (Keychain / env / ~/openai/access_key.txt)\n"
return
fi
if keychain_export OPENAI_API_KEY \
"${OPENAI_KEYCHAIN_ENTRY:-}" \
"OPENAI_API_KEY" "openai" "OpenAI" "openai-api-key"; then
echo " ok: OPENAI_API_KEY resolved"
return
fi
if [[ -f "$HOME/openai/access_key.txt" ]]; then
echo " ok: ~/openai/access_key.txt present (inst/gpt.py will read it)"
return
fi
echo "ERROR: no OpenAI key found. Set OPENAI_API_KEY, add an entry to" >&2
echo " the macOS Keychain (override service name via" >&2
echo " OPENAI_KEYCHAIN_ENTRY=<name>), or place the key at" >&2
echo " ~/openai/access_key.txt." >&2
exit 1
}

# ---------------------------------------------------------------------------
# downloads: shared ontology + tool downloads (robot.jar, CLO, EFO, TGEMO)
# ---------------------------------------------------------------------------
run_downloads() {
run "$RSCRIPT $ANA/_downloads/download.R"
}

# ---------------------------------------------------------------------------
# strains: strain-task pipeline (sequential)
# ---------------------------------------------------------------------------
run_strains() {
run "$RSCRIPT $ANA/strains/00.downloads.R"
run "$RSCRIPT $ANA/strains/01.ask_regex.R"
run "$RSCRIPT $ANA/strains/02.ask_gpt.R"
run "$RSCRIPT $ANA/strains/03.evaluate.R"
run "$RSCRIPT $ANA/strains/04.post_curation.R"
}

# ---------------------------------------------------------------------------
# cells: cell-line pipeline (sequential)
# ---------------------------------------------------------------------------
run_cells() {
run "$RSCRIPT $ANA/cell_lines/00.downloads.R"
run "$RSCRIPT $ANA/cell_lines/01.process_cell_lines.R"
run "$RSCRIPT $ANA/cell_lines/02.ask_gpt.R"
run "$RSCRIPT $ANA/cell_lines/03.compare_to_vect.R"
run "$RSCRIPT $ANA/cell_lines/04.rag_inputs.R"
run "$RSCRIPT $ANA/cell_lines/05.rag_gpt.R"
run "$RSCRIPT $ANA/cell_lines/06.evaluate.R"
run "$RSCRIPT $ANA/cell_lines/07.post_curator_evaluation.R"
}

# ---------------------------------------------------------------------------
# Run the requested phases
# ---------------------------------------------------------------------------
phase keys verify_keys
phase downloads run_downloads
phase strains run_strains
phase cells run_cells

echo
echo "All requested phases finished."