ruvector/examples/data/framework/src/ingester.rs
rUv 38d93a6e8d feat: Add comprehensive dataset discovery framework for RuVector (#104)
* feat: Add comprehensive dataset discovery framework for RuVector

This commit introduces a powerful dataset discovery framework with
integrations for three high-impact public data sources:

## Core Framework (examples/data/framework/)
- DataIngester: Streaming ingestion with batching and deduplication
- CoherenceEngine: Min-cut based coherence signal computation
- DiscoveryEngine: Pattern detection for emerging structures

## OpenAlex Integration (examples/data/openalex/)
- Research frontier radar: Detect emerging fields via boundary motion
- Cross-domain bridge detection: Find connector subgraphs
- Topic graph construction from citation networks
- Full API client with cursor-based pagination

## Climate Integration (examples/data/climate/)
- NOAA GHCN and NASA Earthdata clients
- Sensor network graph construction
- Regime shift detection using min-cut coherence breaks
- Time series vectorization for similarity search
- Seasonal decomposition analysis

## SEC EDGAR Integration (examples/data/edgar/)
- XBRL financial statement parsing
- Peer network construction
- Coherence watch: Detect fundamental vs narrative divergence
- Filing analysis with sentiment and risk extraction
- Cross-company contagion detection

Each integration leverages RuVector's unique capabilities:
- Vector memory for semantic similarity
- Graph structures for relationship modeling
- Dynamic min-cut for coherence signal computation
- Time series embeddings for pattern matching

Discovery thesis: Detect emerging patterns before they have names,
find non-obvious cross-domain bridges, and map causality chains.

* feat: Add working discovery examples for climate and financial data

- Fix borrow checker issues in coherence analysis modules
- Create standalone workspace for data examples
- Add regime_detector.rs for climate network coherence analysis
- Add coherence_watch.rs for SEC EDGAR narrative-fundamental divergence
- Add frontier_radar.rs template for OpenAlex research discovery
- Update Cargo.toml dependencies for example executability
- Add rand dev-dependency for demo data generation

Examples successfully detect:
- Climate regime shifts via min-cut coherence analysis
- Cross-regional teleconnection patterns
- Fundamental vs narrative divergence in SEC filings
- Sector fragmentation signals in financial data

* feat: Add working discovery examples for climate and financial data

- Add RuVector-native discovery engine with Stoer-Wagner min-cut
- Implement cross-domain pattern detection (climate ↔ finance)
- Add cosine similarity for vector-based semantic matching
- Create cross_domain_discovery example demonstrating:
  - 42% cross-domain edge connectivity
  - Bridge formation detection with 0.73-0.76 confidence
  - Climate and finance correlation hypothesis generation

* perf: Add optimized discovery engine with SIMD and parallel processing

Performance improvements:
- 8.84x speedup for vector insertion via parallel batching
- 2.91x SIMD speedup for cosine similarity (chunked + AVX2)
- Incremental graph updates with adjacency caching
- Early termination in Stoer-Wagner min-cut

Statistical analysis features:
- P-value computation for pattern significance
- Effect size (Cohen's d) calculation
- 95% confidence intervals
- Granger-style temporal causality detection

Benchmark results (248 vectors, 3 domains):
- Cross-domain edges: 34.9% of total graph
- Domain coherence: Climate 0.74, Finance 0.94, Research 0.97
- Detected climate-finance temporal correlations

* feat: Add discovery hunter and comprehensive README tutorial

New features:
- Discovery hunter example with multi-phase pattern detection
- Climate extremes, financial stress, and research data generation
- Cross-domain hypothesis generation
- Anomaly injection testing

Documentation:
- Detailed README with step-by-step tutorial
- API reference for OptimizedConfig and patterns
- Performance benchmarks and best practices
- Troubleshooting guide

* feat: Complete discovery framework with all features

HNSW Indexing (754 lines):
- O(log n) approximate nearest neighbor search
- Configurable M, ef_construction parameters
- Cosine, Euclidean, Manhattan distance metrics
- Batch insertion support

API Clients (888 lines):
- OpenAlex: academic works, authors, topics
- NOAA: climate observations
- SEC EDGAR: company filings
- Rate limiting and retry logic

Persistence (638 lines):
- Save/load engine state and patterns
- Gzip compression (3-10x size reduction)
- Incremental pattern appending

CLI Tool (1,109 lines):
- discover, benchmark, analyze, export commands
- Colored terminal output
- JSON and human-readable formats

Streaming (570 lines):
- Async stream processing
- Sliding and tumbling windows
- Real-time pattern detection
- Backpressure handling

Tests (30 unit tests):
- Stoer-Wagner min-cut verification
- SIMD cosine similarity accuracy
- Statistical significance
- Granger causality
- Cross-domain patterns

Benchmarks:
- CLI: 176 vectors/sec @ 2000 vectors
- SIMD: 6.82M ops/sec (2.06x speedup)
- Vector insertion: 1.61x speedup
- Total: 44.74ms for 248 vectors

* feat: Add visualization, export, forecasting, and real data discovery

Visualization (555 lines):
- ASCII graph rendering with box-drawing characters
- Domain-based ANSI coloring (Climate=blue, Finance=green, Research=yellow)
- Coherence timeline sparklines
- Pattern summary dashboard
- Domain connectivity matrix

Export (650 lines):
- GraphML export for Gephi/Cytoscape
- DOT export for Graphviz
- CSV export for patterns and coherence history
- Filtered export by domain, weight, time range
- Batch export with README generation

Forecasting (525 lines):
- Holt's double exponential smoothing for trend
- CUSUM-based regime change detection (70.67% accuracy)
- Cross-domain correlation forecasting (r=1.000)
- Prediction intervals (95% CI)
- Anomaly probability scoring

Real Data Discovery:
- Fetched 80 actual papers from OpenAlex API
- Topics: climate risk, stranded assets, carbon pricing, physical risk, transition risk
- Built coherence graph: 592 nodes, 1049 edges
- Average min-cut: 185.76 (well-connected research cluster)

* feat: Add medical, real-time, and knowledge graph data sources

New API Clients:
- PubMed E-utilities for medical literature search (NCBI)
- ClinicalTrials.gov v2 API for clinical study data
- FDA OpenFDA for drug adverse events and recalls
- Wikipedia article search and extraction
- Wikidata SPARQL queries for structured knowledge

Real-time Features:
- RSS/Atom feed parsing with deduplication
- News aggregator with multiple source support
- WebSocket and REST polling infrastructure
- Event streaming with configurable windows

Examples:
- medical_discovery: PubMed + ClinicalTrials + FDA integration
- multi_domain_discovery: Climate-health-finance triangulation
- wiki_discovery: Wikipedia/Wikidata knowledge graph
- realtime_feeds: News feed aggregation demo

Tested across 70+ unit tests with all domains integrated.

* feat: Add economic, patent, and ArXiv data source clients

New API Clients:
- FredClient: Federal Reserve economic indicators (GDP, CPI, unemployment)
- WorldBankClient: Global development indicators and climate data
- AlphaVantageClient: Stock market daily prices
- ArxivClient: Scientific preprint search with category and date filters
- UsptoPatentClient: USPTO patent search by keyword, assignee, CPC class
- EpoClient: Placeholder for European patent search

New Domain:
- Domain::Economic for economic/financial indicator data

Updated Exports:
- Domain colors and shapes for Economic in visualization and export

Examples:
- economic_discovery: FRED + World Bank integration demo
- arxiv_discovery: AI/ML/Climate paper search demo
- patent_discovery: Climate tech and AI patent search demo

All 85 tests passing. APIs tested with live endpoints.

* feat: Add Semantic Scholar, bioRxiv/medRxiv, and CrossRef research clients

New Research API Clients:
- SemanticScholarClient: Citation graph analysis, paper search, author lookup
  - Methods: search_papers, get_citations, get_references, search_by_field
  - Builds citation networks for graph analysis

- BiorxivClient: Life sciences preprints
  - Methods: search_recent, search_by_category (neuroscience, genomics, etc.)
  - Automatic conversion to Domain::Research

- MedrxivClient: Medical preprints
  - Methods: search_covid, search_clinical, search_by_date_range
  - Automatic conversion to Domain::Medical

- CrossRefClient: DOI metadata and scholarly communication
  - Methods: search_works, get_work, search_by_funder, get_citations
  - Polite pool support for better rate limits

All clients include:
- Rate limiting respecting API guidelines
- Retry logic with exponential backoff
- SemanticVector conversion with rich metadata
- Comprehensive unit tests

Examples:
- biorxiv_discovery: Fetch neuroscience and clinical research
- crossref_demo: Search publications, funders, datasets

Total: 104 tests passing, ~2,500 new lines of code

* feat: Add MCP server with STDIO/SSE transport and optimized discovery

MCP Server Implementation (mcp_server.rs):
- JSON-RPC 2.0 protocol with MCP 2024-11-05 compliance
- Dual transport: STDIO for CLI, SSE for HTTP streaming
- 22 discovery tools exposing all data sources:
  - Research: OpenAlex, ArXiv, Semantic Scholar, CrossRef, bioRxiv, medRxiv
  - Medical: PubMed, ClinicalTrials.gov, FDA
  - Economic: FRED, World Bank
  - Climate: NOAA
  - Knowledge: Wikipedia, Wikidata SPARQL
  - Discovery: Multi-source, coherence analysis, pattern detection
- Resources: discovery://patterns, discovery://graph, discovery://history
- Pre-built prompts: cross_domain_discovery, citation_analysis, trend_detection

Binary Entry Point (bin/mcp_discovery.rs):
- CLI arguments with clap
- Configurable discovery parameters
- STDIO/SSE mode selection

Optimized Discovery Runner:
- Parallel data fetching with tokio::join!
- SIMD-accelerated vector operations (1.1M comparisons/sec)
- 6-phase discovery pipeline with benchmarking
- Statistical significance testing (p-values)
- Cross-domain correlation analysis
- CSV export and hypothesis report generation

Performance Results:
- 180 vectors from 3 sources in 7.5s
- 686 edges computed in 8ms
- SIMD throughput: 1,122,216 comparisons/sec

All 106 tests passing.

* feat: Add space, genomics, and physics data source clients

Add exotic data source integrations:
- Space clients: NASA (APOD, NEO, Mars, DONKI), Exoplanet Archive, SpaceX API, TNS Astronomy
- Genomics clients: NCBI (genes, proteins, SNPs), UniProt, Ensembl, GWAS Catalog
- Physics clients: USGS Earthquakes, CERN Open Data, Argo Ocean, Materials Project

New domains: Space, Genomics, Physics, Seismic, Ocean

All 106 tests passing, SIMD benchmark: 208k comparisons/sec

* chore: Update export/visualization and output files

* docs: Add API client inventory and reference documentation

* fix: Update API clients for 2025 endpoint changes

- ArXiv: Switch from HTTP to HTTPS (export.arxiv.org)
- USPTO: Migrate to PatentSearch API v2 (search.patentsview.org)
  - Legacy API (api.patentsview.org) discontinued May 2025
  - Updated query format from POST to GET
  - Note: May require API authentication
- FRED: Require API key (mandatory as of 2025)
  - Added error handling for missing API key
  - Added response error field parsing

All tests passing, ArXiv discovery confirmed working

* feat: Implement comprehensive 2025 API client library (11,810 lines)

Add 7 new API client modules implementing 35+ data sources:

Academic APIs (1,328 lines):
- OpenAlexClient, CoreClient, EricClient, UnpaywallClient

Finance APIs (1,517 lines):
- FinnhubClient, TwelveDataClient, CoinGeckoClient, EcbClient, BlsClient

Geospatial APIs (1,250 lines):
- NominatimClient, OverpassClient, GeonamesClient, OpenElevationClient

News & Social APIs (1,606 lines):
- HackerNewsClient, GuardianClient, NewsDataClient, RedditClient

Government APIs (2,354 lines):
- CensusClient, DataGovClient, EuOpenDataClient, UkGovClient
- WorldBankGovClient, UNDataClient

AI/ML APIs (2,035 lines):
- HuggingFaceClient, OllamaClient, ReplicateClient
- TogetherAiClient, PapersWithCodeClient

Transportation APIs (1,720 lines):
- GtfsClient, MobilityDatabaseClient
- OpenRouteServiceClient, OpenChargeMapClient

All clients include:
- Async/await with tokio and reqwest
- Mock data fallback for testing without API keys
- Rate limiting with configurable delays
- SemanticVector conversion for RuVector integration
- Comprehensive unit tests (252 total tests passing)
- Full error handling with FrameworkError

* docs: Add API client documentation for new implementations

Add documentation for:
- Geospatial clients (Nominatim, Overpass, Geonames, OpenElevation)
- ML clients (HuggingFace, Ollama, Replicate, Together, PapersWithCode)
- News clients (HackerNews, Guardian, NewsData, Reddit)
- Finance clients implementation notes

* feat: Implement dynamic min-cut tracking system (SODA 2026)

Based on El-Hayek, Henzinger, Li (SODA 2026) subpolynomial dynamic min-cut algorithm.

Core Components (2,626 lines):
- dynamic_mincut.rs (1,579 lines): EulerTourTree, DynamicCutWatcher, LocalMinCutProcedure
- cut_aware_hnsw.rs (1,047 lines): CutAwareHNSW, CoherenceZones, CutGatedSearch

Key Features:
- O(log n) connectivity queries via Euler-tour trees
- n^{o(1)} update time when λ ≤ 2^{(log n)^{3/4}} (vs O(n³) Stoer-Wagner)
- Cut-gated HNSW search that respects coherence boundaries
- Real-time cut monitoring with threshold-based deep evaluation
- Thread-safe structures with Arc<RwLock>

Performance (benchmarked):
- 75x speedup over periodic recomputation
- O(1) min-cut queries vs O(n³) recompute
- ~25µs per edge update

Tests & Benchmarks:
- 36+ unit tests across both modules
- 5 benchmark suites comparing periodic vs dynamic
- Integration with existing OptimizedDiscoveryEngine

This enables real-time coherence tracking in RuVector, transforming
min-cut from an expensive periodic computation to a maintained invariant.

---------

Co-authored-by: Claude <noreply@anthropic.com>
2026-01-04 14:36:41 -05:00

342 lines
9.3 KiB
Rust

//! Data ingestion pipeline for streaming data into RuVector
use std::collections::HashMap;
use std::sync::Arc;
use async_trait::async_trait;
use serde::{Deserialize, Serialize};
use tokio::sync::mpsc;
use crate::{DataRecord, DataSource, FrameworkError, Result};
/// Configuration for data ingestion
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct IngestionConfig {
/// Batch size for fetching
pub batch_size: usize,
/// Maximum concurrent fetches
pub max_concurrent: usize,
/// Retry count on failure
pub retry_count: u32,
/// Delay between retries (ms)
pub retry_delay_ms: u64,
/// Enable deduplication
pub deduplicate: bool,
/// Rate limit (requests per second, 0 = unlimited)
pub rate_limit: u32,
}
impl Default for IngestionConfig {
fn default() -> Self {
Self {
batch_size: 1000,
max_concurrent: 4,
retry_count: 3,
retry_delay_ms: 1000,
deduplicate: true,
rate_limit: 10,
}
}
}
/// Configuration for a specific data source
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct SourceConfig {
/// Source identifier
pub source_id: String,
/// API base URL
pub base_url: String,
/// API key (if required)
pub api_key: Option<String>,
/// Additional headers
pub headers: HashMap<String, String>,
/// Custom parameters
pub params: HashMap<String, String>,
}
/// Statistics for ingestion process
#[derive(Debug, Clone, Default, Serialize, Deserialize)]
pub struct IngestionStats {
/// Total records fetched
pub records_fetched: u64,
/// Batches processed
pub batches_processed: u64,
/// Retries performed
pub retries: u64,
/// Errors encountered
pub errors: u64,
/// Duplicates skipped
pub duplicates_skipped: u64,
/// Bytes downloaded
pub bytes_downloaded: u64,
/// Average batch fetch time (ms)
pub avg_batch_time_ms: f64,
}
/// Data ingestion pipeline
pub struct DataIngester {
config: IngestionConfig,
stats: Arc<std::sync::RwLock<IngestionStats>>,
seen_ids: Arc<std::sync::RwLock<std::collections::HashSet<String>>>,
}
impl DataIngester {
/// Create a new data ingester
pub fn new(config: IngestionConfig) -> Self {
Self {
config,
stats: Arc::new(std::sync::RwLock::new(IngestionStats::default())),
seen_ids: Arc::new(std::sync::RwLock::new(std::collections::HashSet::new())),
}
}
/// Ingest all data from a source
pub async fn ingest_all<S: DataSource>(&self, source: &S) -> Result<Vec<DataRecord>> {
let mut all_records = Vec::new();
let mut cursor: Option<String> = None;
loop {
let (batch, next_cursor) = self
.fetch_with_retry(source, cursor.clone(), self.config.batch_size)
.await?;
if batch.is_empty() {
break;
}
// Deduplicate if enabled
let records = if self.config.deduplicate {
self.deduplicate_batch(batch)
} else {
batch
};
all_records.extend(records);
{
let mut stats = self.stats.write().unwrap();
stats.batches_processed += 1;
}
cursor = next_cursor;
if cursor.is_none() {
break;
}
// Rate limiting
if self.config.rate_limit > 0 {
let delay = 1000 / self.config.rate_limit as u64;
tokio::time::sleep(tokio::time::Duration::from_millis(delay)).await;
}
}
Ok(all_records)
}
/// Stream records with backpressure
pub async fn stream_records<S: DataSource + 'static>(
&self,
source: Arc<S>,
buffer_size: usize,
) -> Result<mpsc::Receiver<DataRecord>> {
let (tx, rx) = mpsc::channel(buffer_size);
let config = self.config.clone();
let stats = self.stats.clone();
let seen_ids = self.seen_ids.clone();
tokio::spawn(async move {
let mut cursor: Option<String> = None;
loop {
match source
.fetch_batch(cursor.clone(), config.batch_size)
.await
{
Ok((batch, next_cursor)) => {
if batch.is_empty() {
break;
}
for record in batch {
// Deduplicate
if config.deduplicate {
let mut ids = seen_ids.write().unwrap();
if ids.contains(&record.id) {
continue;
}
ids.insert(record.id.clone());
}
if tx.send(record).await.is_err() {
return; // Receiver dropped
}
let mut s = stats.write().unwrap();
s.records_fetched += 1;
}
cursor = next_cursor;
if cursor.is_none() {
break;
}
}
Err(_) => {
let mut s = stats.write().unwrap();
s.errors += 1;
break;
}
}
}
});
Ok(rx)
}
/// Fetch a batch with retry logic
async fn fetch_with_retry<S: DataSource>(
&self,
source: &S,
cursor: Option<String>,
batch_size: usize,
) -> Result<(Vec<DataRecord>, Option<String>)> {
let mut last_error = None;
for attempt in 0..=self.config.retry_count {
if attempt > 0 {
let delay = self.config.retry_delay_ms * (1 << (attempt - 1));
tokio::time::sleep(tokio::time::Duration::from_millis(delay)).await;
let mut stats = self.stats.write().unwrap();
stats.retries += 1;
}
match source.fetch_batch(cursor.clone(), batch_size).await {
Ok(result) => return Ok(result),
Err(e) => {
last_error = Some(e);
}
}
}
let mut stats = self.stats.write().unwrap();
stats.errors += 1;
Err(last_error.unwrap_or_else(|| FrameworkError::Ingestion("Unknown error".to_string())))
}
/// Deduplicate a batch of records
fn deduplicate_batch(&self, batch: Vec<DataRecord>) -> Vec<DataRecord> {
let mut unique = Vec::with_capacity(batch.len());
let mut seen = self.seen_ids.write().unwrap();
for record in batch {
if !seen.contains(&record.id) {
seen.insert(record.id.clone());
unique.push(record);
} else {
let mut stats = self.stats.write().unwrap();
stats.duplicates_skipped += 1;
}
}
unique
}
/// Get current ingestion statistics
pub fn stats(&self) -> IngestionStats {
self.stats.read().unwrap().clone()
}
/// Reset statistics
pub fn reset_stats(&self) {
*self.stats.write().unwrap() = IngestionStats::default();
}
}
/// Trait for transforming records during ingestion
#[async_trait]
pub trait RecordTransformer: Send + Sync {
/// Transform a record
async fn transform(&self, record: DataRecord) -> Result<DataRecord>;
/// Filter records (return false to skip)
fn filter(&self, record: &DataRecord) -> bool {
true
}
}
/// Identity transformer (no-op)
pub struct IdentityTransformer;
#[async_trait]
impl RecordTransformer for IdentityTransformer {
async fn transform(&self, record: DataRecord) -> Result<DataRecord> {
Ok(record)
}
}
/// Batched ingestion with transformations
pub struct BatchIngester<T: RecordTransformer> {
ingester: DataIngester,
transformer: T,
}
impl<T: RecordTransformer> BatchIngester<T> {
/// Create a new batch ingester with transformer
pub fn new(config: IngestionConfig, transformer: T) -> Self {
Self {
ingester: DataIngester::new(config),
transformer,
}
}
/// Ingest and transform all records
pub async fn ingest_all<S: DataSource>(&self, source: &S) -> Result<Vec<DataRecord>> {
let raw_records = self.ingester.ingest_all(source).await?;
let mut transformed = Vec::with_capacity(raw_records.len());
for record in raw_records {
if self.transformer.filter(&record) {
let t = self.transformer.transform(record).await?;
transformed.push(t);
}
}
Ok(transformed)
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_default_config() {
let config = IngestionConfig::default();
assert_eq!(config.batch_size, 1000);
assert!(config.deduplicate);
}
#[test]
fn test_ingester_creation() {
let config = IngestionConfig::default();
let ingester = DataIngester::new(config);
let stats = ingester.stats();
assert_eq!(stats.records_fetched, 0);
}
}