mirror of
https://github.com/allaunthefox/Research-Stack.git
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ac4e23dc9b
- .devcontainer/Dockerfile: add PostgreSQL client libs, OpenSSL/libffi headers, gfortran/BLAS for scipy, rclone; install full Python dependency set (boto3, psycopg2-binary, fastapi, uvicorn, notion-client, httpx, pytest, numpy, scipy, etc.) in uv-managed venv; add rclone S3 gateway init script as ENTRYPOINT - .devcontainer/devcontainer.json: switch from build to pre-built image (localhost/research
605 lines
23 KiB
Python
605 lines
23 KiB
Python
#!/usr/bin/env python3
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"""
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Bulk dataset ingestion → Aurora PostgreSQL.
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Sources:
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1. consolidated equations bundle (equations/refs/links/dois/articles)
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2. consolidated dataset inventory (161-file artifact manifest)
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3. TiddlyWiki tiddlers (263 .tid files)
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4. Γ-packet seed data
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Each run recorded in ingestion.receipts.
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Run inside the dev container:
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podman exec -i research-stack python3 /home/researcher/stack/4-Infrastructure/shim/dataset_ingest_rds.py
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"""
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from __future__ import annotations
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import hashlib
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import json
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import logging
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import os
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import sys
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import uuid
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from datetime import datetime, timezone
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from pathlib import Path
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import boto3
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import psycopg2
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import psycopg2.extras
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logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
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log = logging.getLogger("dataset_ingest_rds")
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# Config
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RDS_HOST = os.environ.get("RDS_HOST", "database-1-instance-1.cghu8yqogqwo.us-east-1.rds.amazonaws.com")
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RDS_PORT = int(os.environ.get("RDS_PORT", "5432"))
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RDS_USER = os.environ.get("RDS_USER", "postgres")
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RDS_DBNAME = os.environ.get("RDS_DBNAME", "postgres")
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RDS_IAM = os.environ.get("RDS_IAM", "1") == "1"
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RDS_PW = os.environ.get("RDS_PASSWORD", "")
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AWS_REGION = os.environ.get("AWS_REGION", "us-east-1")
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STACK_ROOT = Path(os.environ.get("STACK_ROOT", "/home/researcher/stack"))
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DATA_DIR = STACK_ROOT / "shared-data" / "data" / "ingested_datasets" / "2026-05-18"
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BUNDLE_EQS = DATA_DIR / "consolidated_links_bibtex_latex_articles_equations_2026_05_18"
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BUNDLE_INV = DATA_DIR / "consolidated_ingested_datasets_2026_05_18"
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TIDDLYWIKI_DIR = STACK_ROOT / "6-Documentation" / "tiddlywiki-local" / "wiki" / "tiddlers"
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# ---------------------------------------------------------------------------
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# DB
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# ---------------------------------------------------------------------------
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def get_db_password() -> str:
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if RDS_IAM:
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client = boto3.client("rds", region_name=AWS_REGION)
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return client.generate_db_auth_token(
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DBHostname=RDS_HOST, Port=RDS_PORT, DBUsername=RDS_USER, Region=AWS_REGION,
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)
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return RDS_PW
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def connect():
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pw = get_db_password()
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return psycopg2.connect(
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host=RDS_HOST, port=RDS_PORT, user=RDS_USER,
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password=pw, dbname=RDS_DBNAME, sslmode="require",
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)
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def ensure_schema(conn):
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cur = conn.cursor()
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# Equations and references
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cur.execute("""
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CREATE TABLE IF NOT EXISTS knowledge.equations (
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eq_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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latex text NOT NULL,
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kind text NOT NULL DEFAULT 'display',
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source_file text NOT NULL,
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source_offset integer,
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content_hash text NOT NULL,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE INDEX IF NOT EXISTS eq_source_idx ON knowledge.equations (source_file);
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CREATE INDEX IF NOT EXISTS eq_hash_idx ON knowledge.equations (content_hash);
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CREATE TABLE IF NOT EXISTS knowledge.references (
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ref_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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bibtex text NOT NULL,
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source_file text NOT NULL,
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source_offset integer,
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content_hash text NOT NULL,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE TABLE IF NOT EXISTS knowledge.links (
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link_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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url text NOT NULL,
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source_file text NOT NULL,
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source_offset integer,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE TABLE IF NOT EXISTS knowledge.dois (
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doi_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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doi text NOT NULL UNIQUE,
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source_file text NOT NULL,
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source_offset integer,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE TABLE IF NOT EXISTS knowledge.article_sources (
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article_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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url text NOT NULL,
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label text,
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category text,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE TABLE IF NOT EXISTS knowledge.tiddlywiki_pages (
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tiddler_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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title text NOT NULL,
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tags text,
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created text,
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modified text,
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body text,
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source_path text NOT NULL,
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content_hash text NOT NULL,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE INDEX IF NOT EXISTS tw_title_idx ON knowledge.tiddlywiki_pages (title);
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CREATE TABLE IF NOT EXISTS knowledge.dataset_inventory (
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inv_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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asset_id text NOT NULL,
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name text,
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kind text,
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status text,
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evidence text,
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local_paths text,
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notes text,
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ingested_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE TABLE IF NOT EXISTS knowledge.ingestion_runs (
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run_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
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source_name text NOT NULL,
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total_items integer NOT NULL DEFAULT 0,
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items_ingested integer NOT NULL DEFAULT 0,
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items_skipped integer NOT NULL DEFAULT 0,
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error_detail text,
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ran_at timestamptz NOT NULL DEFAULT now()
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);
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CREATE TABLE IF NOT EXISTS knowledge.gamma_packets (
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component_id text PRIMARY KEY,
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component_label text NOT NULL,
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category text NOT NULL,
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X_input_name text,
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pi_projection_name text,
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W_result_name text,
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R_receipt_name text,
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I_constraints_name text,
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G_guards_name text,
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K_cost_name text,
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epsilon_residual_name text,
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source_doc text,
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source_url text,
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citation_bibtex text,
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parent_component text,
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family text,
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doc_section text,
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famm_object text,
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famm_residual_formula text,
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receipt text NOT NULL,
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tags jsonb NOT NULL DEFAULT '[]',
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created_at timestamptz NOT NULL DEFAULT now(),
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updated_at timestamptz NOT NULL DEFAULT now(),
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allowed_claim text,
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disallowed_claim text,
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hard_rules jsonb NOT NULL DEFAULT '[]',
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project_sentence text
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);
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CREATE TABLE IF NOT EXISTS knowledge.gamma_components (
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component_id text NOT NULL REFERENCES knowledge.gamma_packets(component_id) ON DELETE CASCADE,
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slot_name text NOT NULL,
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slot_index smallint NOT NULL CHECK (slot_index BETWEEN 1 AND 8),
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local_symbol text,
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field_name text,
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meaning text,
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json_schema jsonb DEFAULT '{}',
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example_value jsonb DEFAULT '{}',
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per_key_slot boolean NOT NULL DEFAULT false,
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retention_rule text,
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PRIMARY KEY (component_id, slot_name)
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);
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CREATE TABLE IF NOT EXISTS knowledge.implementation_tiers (
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component_id text NOT NULL REFERENCES knowledge.gamma_packets(component_id) ON DELETE CASCADE,
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tier_number smallint NOT NULL CHECK (tier_number BETWEEN 0 AND 6),
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tier_label text NOT NULL,
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tier_description text,
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status text NOT NULL DEFAULT 'planned',
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prerequisite text,
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depended_on_by text[],
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receipt_sha256 text,
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verified_at timestamptz,
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created_at timestamptz NOT NULL DEFAULT now(),
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updated_at timestamptz NOT NULL DEFAULT now(),
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PRIMARY KEY (component_id, tier_number)
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);
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CREATE TABLE IF NOT EXISTS ingestion.receipts (
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receipt_id uuid PRIMARY KEY,
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shim_name text NOT NULL,
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status text NOT NULL,
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metadata jsonb NOT NULL DEFAULT '{}',
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error_detail text,
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ran_at timestamptz NOT NULL DEFAULT now()
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);
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""")
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conn.commit()
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log.info("Schema ready")
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def record_run(conn, source_name: str, total: int, ingested: int, skipped: int, error: str | None = None):
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with conn.cursor() as cur:
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cur.execute(
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"""INSERT INTO knowledge.ingestion_runs
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(source_name, total_items, items_ingested, items_skipped, error_detail)
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VALUES (%s,%s,%s,%s,%s)""",
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(source_name, total, ingested, skipped, error),
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)
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conn.commit()
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def record_receipt(conn, shim: str, status: str, metadata: dict, error: str | None = None):
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with conn.cursor() as cur:
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cur.execute(
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"""INSERT INTO ingestion.receipts
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(receipt_id, shim_name, status, metadata, error_detail, ran_at)
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VALUES (%s,%s,%s,%s,%s,now())""",
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(str(uuid.uuid4()), shim, status, json.dumps(metadata), error),
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)
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conn.commit()
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# ---------------------------------------------------------------------------
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# Ingestion functions
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# ---------------------------------------------------------------------------
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def load_jsonl(path: Path) -> list:
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"""Load json or jsonl file."""
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with open(path, "r") as f:
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data = json.load(f)
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return data if isinstance(data, list) else []
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def ingest_equations(conn) -> tuple[int, int]:
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"""Ingest equations.json → knowledge.equations"""
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fpath = BUNDLE_EQS / "equations.json"
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if not fpath.exists():
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return 0, 0
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items = load_jsonl(fpath)
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if not items:
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for eq in items:
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latex = eq.get("latex", "").strip()
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if not latex:
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skipped += 1
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continue
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chash = hashlib.sha256(latex.encode()).hexdigest()
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cur.execute(
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"""INSERT INTO knowledge.equations (latex, kind, source_file, source_offset, content_hash)
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VALUES (%s,%s,%s,%s,%s)
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ON CONFLICT DO NOTHING""",
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(latex, eq.get("kind", "display"), eq.get("source_file", ""),
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eq.get("offset"), chash),
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)
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if cur.rowcount > 0:
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ingested += 1
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else:
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skipped += 1
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conn.commit()
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log.info("Equations: %d ingested, %d skipped", ingested, skipped)
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return ingested, skipped
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def ingest_references(conn) -> tuple[int, int]:
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"""Ingest references.json → knowledge.references"""
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fpath = BUNDLE_EQS / "references.json"
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if not fpath.exists():
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return 0, 0
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items = load_jsonl(fpath)
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if not items:
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for r in items:
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bibtex = r.get("bibtex", "").strip()
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if not bibtex:
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skipped += 1
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continue
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chash = hashlib.sha256(bibtex.encode()).hexdigest()
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cur.execute(
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"""INSERT INTO knowledge.references (bibtex, source_file, source_offset, content_hash)
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VALUES (%s,%s,%s,%s)
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ON CONFLICT DO NOTHING""",
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(bibtex, r.get("source_file", ""), r.get("offset"), chash),
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)
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if cur.rowcount > 0:
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ingested += 1
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else:
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skipped += 1
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conn.commit()
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log.info("References: %d ingested, %d skipped", ingested, skipped)
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return ingested, skipped
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def ingest_links(conn) -> tuple[int, int]:
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"""Ingest links.json → knowledge.links"""
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fpath = BUNDLE_EQS / "links.json"
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if not fpath.exists():
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return 0, 0
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items = load_jsonl(fpath)
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if not items:
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for r in items:
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url = r.get("url", "").strip()
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if not url:
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skipped += 1
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continue
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cur.execute(
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"""INSERT INTO knowledge.links (url, source_file, source_offset)
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VALUES (%s,%s,%s)
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ON CONFLICT DO NOTHING""",
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(url, r.get("source_file", ""), r.get("offset")),
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)
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if cur.rowcount > 0:
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ingested += 1
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else:
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skipped += 1
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conn.commit()
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log.info("Links: %d ingested, %d skipped", ingested, skipped)
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return ingested, skipped
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def ingest_dois(conn) -> tuple[int, int]:
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"""Ingest dois.json → knowledge.dois"""
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fpath = BUNDLE_EQS / "dois.json"
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if not fpath.exists():
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return 0, 0
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items = load_jsonl(fpath)
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if not items:
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for r in items:
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doi = r.get("doi", "").strip()
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if not doi:
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skipped += 1
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continue
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cur.execute(
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"""INSERT INTO knowledge.dois (doi, source_file, source_offset)
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VALUES (%s,%s,%s)
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ON CONFLICT (doi) DO NOTHING""",
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(doi, r.get("source_file", ""), r.get("offset")),
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)
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if cur.rowcount > 0:
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ingested += 1
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else:
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skipped += 1
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conn.commit()
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log.info("DOIs: %d ingested, %d skipped", ingested, skipped)
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return ingested, skipped
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def ingest_article_sources(conn) -> tuple[int, int]:
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"""Ingest articles_sources.json → knowledge.article_sources"""
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fpath = BUNDLE_EQS / "articles_sources.json"
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if not fpath.exists():
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return 0, 0
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items = load_jsonl(fpath)
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if not items:
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for r in items:
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url = r.get("url", "").strip()
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if not url:
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skipped += 1
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continue
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cur.execute(
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"""INSERT INTO knowledge.article_sources (url, label, category)
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VALUES (%s,%s,%s)
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ON CONFLICT DO NOTHING""",
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(url, r.get("label", ""), r.get("category", "")),
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)
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if cur.rowcount > 0:
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ingested += 1
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else:
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skipped += 1
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conn.commit()
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log.info("Article sources: %d ingested, %d skipped", ingested, skipped)
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return ingested, skipped
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def ingest_dataset_inventory(conn) -> tuple[int, int]:
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"""Ingest dataset_inventory.json → knowledge.dataset_inventory"""
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fpath = BUNDLE_INV / "manifest" / "dataset_inventory.json"
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if not fpath.exists():
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return 0, 0
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items = load_jsonl(fpath)
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if not items:
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for r in items:
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asset_id = r.get("id", "").strip()
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if not asset_id:
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skipped += 1
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continue
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cur.execute(
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"""INSERT INTO knowledge.dataset_inventory
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(asset_id, name, kind, status, evidence, local_paths, notes)
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VALUES (%s,%s,%s,%s,%s,%s,%s)
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ON CONFLICT DO NOTHING""",
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(asset_id, r.get("name", ""), r.get("kind", ""),
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r.get("status", ""), r.get("evidence", ""),
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r.get("local_paths_observed", ""), r.get("notes", "")),
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)
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if cur.rowcount > 0:
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ingested += 1
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else:
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skipped += 1
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conn.commit()
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log.info("Dataset inventory: %d ingested, %d skipped", ingested, skipped)
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return ingested, skipped
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def ingest_tiddlywiki(conn) -> tuple[int, int]:
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"""Ingest 263 .tid files → knowledge.tiddlywiki_pages"""
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if not TIDDLYWIKI_DIR.exists():
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log.warning("TiddlyWiki dir not found: %s", TIDDLYWIKI_DIR)
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return 0, 0
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ingested = 0
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skipped = 0
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with conn.cursor() as cur:
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for fpath in sorted(TIDDLYWIKI_DIR.glob("*.tid")):
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try:
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text = fpath.read_text(encoding="utf-8", errors="replace")
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except Exception:
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skipped += 1
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continue
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# Parse TiddlyWiki fields
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metadata: dict[str, str] = {}
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body_lines: list[str] = []
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in_body = False
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for line in text.split("\n"):
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if not in_body:
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if line.strip() == "":
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in_body = True
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continue
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if ":" in line:
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key, _, val = line.partition(":")
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metadata[key.strip().lower()] = val.strip()
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else:
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body_lines.append(line)
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body = "\n".join(body_lines).strip()
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title = metadata.get("title", fpath.stem)
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chash = hashlib.sha256(body.encode()).hexdigest()
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# Skip system tiddlers ($:/)
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if title.startswith("$:"):
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skipped += 1
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continue
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cur.execute(
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"""INSERT INTO knowledge.tiddlywiki_pages
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(title, tags, created, modified, body, source_path, content_hash)
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VALUES (%s,%s,%s,%s,%s,%s,%s)
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ON CONFLICT DO NOTHING""",
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(title, metadata.get("tags", ""), metadata.get("created", ""),
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metadata.get("modified", ""), body, str(fpath), chash),
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|
)
|
|
if cur.rowcount > 0:
|
|
ingested += 1
|
|
else:
|
|
skipped += 1
|
|
if ingested % 50 == 0:
|
|
conn.commit()
|
|
conn.commit()
|
|
log.info("TiddlyWiki: %d ingested, %d skipped (system)", ingested, skipped)
|
|
return ingested, skipped
|
|
|
|
|
|
def seed_gamma_packets(conn) -> tuple[int, int]:
|
|
"""Seed the 14 known Gamma packets. Existing rows are left alone."""
|
|
packets = [
|
|
("ORToolsWASM", "OR-Tools WASM Constraint Solver Gate", "execution",
|
|
"OR_TOOLS_WASM_CONSTRAINT_SOLVER_GATE.md", "constraint-solver,wasm,cp-sat"),
|
|
("GliaMemory", "GLIA Persistent Memory Substrate", "memory",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES.md", "memory,local-first"),
|
|
("SmallCode", "SmallCode Constrained Execution Substrate", "execution",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES.md", "coding,constrained,patch-first"),
|
|
("NSpaceKV", "N-Space Key-Value Reward Memory", "memory",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "key-value,reward,sparsity"),
|
|
("Collapse", "Field Collapse / Compression Gate", "routing",
|
|
"OR_TOOLS_WASM_CONSTRAINT_SOLVER_GATE.md", "compression,collapse,field-reduction"),
|
|
("MMRGossip", "N-Folded MMR Gossip KV-Cache Surface", "memory",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "mmr,gossip,kv-cache"),
|
|
("Hermes", "Hermes Agent Field Operator Bridge", "governance",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "governance,authority,bridge"),
|
|
("AntiFAMM", "Anti-FAMM Witness Blind-Spot Adversary", "adversarial",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES.md", "adversarial,famm,blind-spot"),
|
|
("AntiBraidStorm", "Anti-BraidStorm Hostile Crossing Adversary", "adversarial",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES.md", "adversarial,braidstorm,alias"),
|
|
("BridgeModel", "BridgeModel Global Gate and Linter", "governance",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "governance,gate,linter"),
|
|
("FastPatchCheck", "FastPatchCheck — Local Viability", "verification",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "verification,patch,smoke-test"),
|
|
("StructuralAdmissibilityCheck", "StructuralAdmissibility — Invariant Legitimacy", "verification",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "verification,admissibility,invariant"),
|
|
("GCLCombined", "GCL Combined Coding Surface", "coding",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "coding,surface,gcl"),
|
|
("LogogramChirality", "Logogram Chirality Route Gate", "routing",
|
|
"POSSIBLE_CONSTRAINED_AGENT_APPROACHES_DEEP_DIVE.md", "logogram,chirality,route"),
|
|
]
|
|
ingested = 0
|
|
with conn.cursor() as cur:
|
|
for cid, label, cat, src, tagstr in packets:
|
|
cur.execute(
|
|
"""INSERT INTO knowledge.gamma_packets
|
|
(component_id, component_label, category, source_doc, tags, receipt)
|
|
VALUES (%s,%s,%s,%s,%s,%s)
|
|
ON CONFLICT (component_id) DO NOTHING""",
|
|
(cid, label, cat, src, json.dumps(tagstr.split(",")),
|
|
f"sha256:{cid}_seed_2026-05-18"),
|
|
)
|
|
if cur.rowcount > 0:
|
|
ingested += 1
|
|
conn.commit()
|
|
log.info("Gamma packets: %d seeded", ingested)
|
|
return ingested, 0
|
|
|
|
|
|
# ---------------------------------------------------------------------------
|
|
# Main
|
|
# ---------------------------------------------------------------------------
|
|
def main():
|
|
log.info("Connecting to RDS (host=%s)…", RDS_HOST)
|
|
conn = connect()
|
|
conn.autocommit = False
|
|
ensure_schema(conn)
|
|
|
|
total_ingested = 0
|
|
total_skipped = 0
|
|
errors: list[str] = []
|
|
|
|
sources = [
|
|
("equations", ingest_equations),
|
|
("references", ingest_references),
|
|
("links", ingest_links),
|
|
("dois", ingest_dois),
|
|
("article_sources", ingest_article_sources),
|
|
("dataset_inventory", ingest_dataset_inventory),
|
|
("tiddlywiki", ingest_tiddlywiki),
|
|
("gamma_packets", seed_gamma_packets),
|
|
]
|
|
|
|
for name, fn in sources:
|
|
try:
|
|
ing, skp = fn(conn)
|
|
total_ingested += ing
|
|
total_skipped += skp
|
|
record_run(conn, name, ing + skp, ing, skp)
|
|
record_receipt(conn, f"dataset_ingest/{name}", "success" if ing > 0 else "empty",
|
|
{"ingested": ing, "skipped": skp})
|
|
except Exception as e:
|
|
msg = str(e)
|
|
log.error("%s ingestion failed: %s", name, msg)
|
|
errors.append(f"{name}: {msg}")
|
|
conn.rollback()
|
|
record_receipt(conn, f"dataset_ingest/{name}", "error", {}, error=msg)
|
|
record_run(conn, name, 0, 0, 0, msg)
|
|
|
|
conn.close()
|
|
log.info("Done. Total ingested=%d skipped=%d errors=%d", total_ingested, total_skipped, len(errors))
|
|
if errors:
|
|
sys.exit(1)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|