scripts/build_metadata_v2.py

#!/usr/bin/env python3
"""
Build dataset_metadata_v2.json from the existing v1 metadata, applying:
  1. ULS23 sub-source routing via case-id prefix (ontology_v2.json)
  2. Per-prompt synonymous augmentation expansion (prompts_augmented.json)
     -> each (case, label) sample carries a list of 7 augmented prompts

Output schema is backward compatible with v1: each sample has 'text_prompts' list.
The training-side change is to randomly sample one prompt per __getitem__ epoch.
"""
from __future__ import annotations
import json
import os
import sys
from pathlib import Path

ROOT = Path("/dgx1data/res/azradonc/m338067/BiomedParse/OmniTumorData")

V1_PATH        = ROOT / "dataset_metadata.json"
ONTOLOGY_V2    = ROOT / "ontology_v2.json"
AUG_PATH       = ROOT / "prompts_augmented.json"
OUT_PATH       = ROOT / "dataset_metadata_v2.json"


def route_uls23_prompt(case_id: str, dataset_name: str, ontology_v2: dict) -> str | None:
    """Return the canonical specific-object prompt for a ULS23 case based on
    its filename prefix; None if the dataset is not ULS23."""
    ds = ontology_v2["datasets"].get(dataset_name)
    if not ds or "case_prefix_routing" not in ds:
        return None
    for rule in ds["case_prefix_routing"]:
        if case_id.startswith(rule["prefix"]):
            return rule["label_1"]
    raise ValueError(f"unknown ULS23 case prefix: {case_id} in {dataset_name}")


def main() -> None:
    v1 = json.loads(V1_PATH.read_text())
    ont = json.loads(ONTOLOGY_V2.read_text())
    aug = json.loads(AUG_PATH.read_text())["augmentations"]

    # 1. Patch top-level 'datasets' block to mirror ontology_v2 canonical labels
    new_datasets = {}
    for ds_name, ds_info in v1["datasets"].items():
        new_ds = dict(ds_info)
        if ds_name in ont["datasets"]:
            ont_ds = ont["datasets"][ds_name]
            if "labels" in ont_ds:
                # static labels: copy text_prompt verbatim from ontology_v2
                for lid, ldat in new_ds["labels"].items():
                    if lid in ont_ds["labels"]:
                        ldat["text_prompt"] = ont_ds["labels"][lid]
            elif "case_prefix_routing" in ont_ds:
                # dynamic per-case routing: drop static text_prompt; mark as routed
                for lid, ldat in new_ds["labels"].items():
                    ldat["text_prompt"] = "<routed_per_case>"
                new_ds["case_prefix_routing"] = ont_ds["case_prefix_routing"]
        new_datasets[ds_name] = new_ds

    # 2. Rewrite samples with per-case canonical prompt + 7-variation augmentation
    new_samples = []
    routed_counts: dict[str, int] = {}
    for s in v1["samples"]:
        ds_name = s["dataset"]
        case_id = s["case_id"]

        # determine canonical prompt(s) per label
        ont_ds = ont["datasets"].get(ds_name, {})
        if "case_prefix_routing" in ont_ds:
            canonical = route_uls23_prompt(case_id, ds_name, ont)
            routed_counts[canonical] = routed_counts.get(canonical, 0) + 1
            # ULS23 currently has only label==1 in v1 metadata
            label_to_canonical = {lid: canonical for lid in s["labels"]}
        else:
            label_to_canonical = {}
            for lid in s["labels"]:
                label_to_canonical[lid] = ont_ds.get("labels", {}).get(str(lid)) \
                    or v1["datasets"][ds_name]["labels"][str(lid)]["text_prompt"]

        # Build a *flat* augmented prompt pool combining all labels' canonicals
        # (most cases have 1 label; BraTS has 3 — at training time __getitem__
        # already creates one (case, label) sample per label, so we keep
        # per-label augmented lists)
        augmented_per_label: dict[str, list[str]] = {}
        for lid, canonical in label_to_canonical.items():
            variations = aug.get(canonical)
            if not variations:
                raise KeyError(f"no augmentation entry for canonical: {canonical}")
            augmented_per_label[str(lid)] = variations  # list of 7 strings

        new_s = dict(s)
        new_s["augmented_prompts_per_label"] = augmented_per_label
        # back-compat: keep 'text_prompts' as the canonical-only list
        new_s["text_prompts"] = [label_to_canonical[lid] for lid in s["labels"]]
        new_samples.append(new_s)

    out = {
        "version": "2.0",
        "description": (
            "v2: ULS23 cases routed by filename prefix to specific objects "
            "(21 unique); each (case, label) carries a list of 7 augmented "
            "prompt variations sampled uniformly at training time."
        ),
        "datasets": new_datasets,
        "samples": new_samples,
        "splits": v1["splits"],
        "summary": v1["summary"],
        "ontology_v2_specific_objects": ont["unique_specific_objects"],
        "uls23_routing_counts": routed_counts,
    }

    OUT_PATH.write_text(json.dumps(out, indent=2))
    print(f"wrote: {OUT_PATH}")
    print(f"samples: {len(new_samples)}")
    print(f"unique specific objects: {len(ont['unique_specific_objects'])}")
    print(f"unique training strings: {sum(len(v) for v in aug.values())}")
    print("ULS23 routing counts:")
    for k, v in sorted(routed_counts.items(), key=lambda x: -x[1]):
        print(f"  {v:>5}  {k}")


if __name__ == "__main__":
    main()