ruvector/examples/data/openalex/src/client.rs
rUv b07fb3e804
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

267 lines
7.8 KiB
Rust

//! OpenAlex API client
use std::time::Duration;
use reqwest::{Client, StatusCode};
use serde::Deserialize;
use crate::{OpenAlexError, Work};
/// OpenAlex API client
pub struct OpenAlexClient {
client: Client,
base_url: String,
email: Option<String>,
}
/// API response wrapper
#[derive(Debug, Deserialize)]
pub struct ApiResponse<T> {
/// Metadata
pub meta: ApiMeta,
/// Results
pub results: Vec<T>,
}
/// API metadata
#[derive(Debug, Deserialize)]
pub struct ApiMeta {
/// Total count
pub count: u64,
/// Current page
pub page: Option<u32>,
/// Results per page
pub per_page: Option<u32>,
/// Next cursor (for cursor-based pagination)
pub next_cursor: Option<String>,
}
impl OpenAlexClient {
/// Create a new OpenAlex client
///
/// Providing an email enables the "polite pool" with higher rate limits.
pub fn new(email: Option<String>) -> Self {
let client = Client::builder()
.timeout(Duration::from_secs(30))
.user_agent("RuVector/0.1.0")
.gzip(true)
.build()
.expect("Failed to build HTTP client");
Self {
client,
base_url: "https://api.openalex.org".to_string(),
email,
}
}
/// Set custom base URL (for testing)
pub fn with_base_url(mut self, url: &str) -> Self {
self.base_url = url.to_string();
self
}
/// Build URL with email parameter
fn build_url(&self, endpoint: &str, params: &str) -> String {
let mut url = format!("{}/{}?{}", self.base_url, endpoint, params);
if let Some(ref email) = self.email {
if !params.is_empty() {
url.push('&');
}
url.push_str(&format!("mailto={}", email));
}
url
}
/// Health check - verify API is accessible
pub async fn health_check(&self) -> Result<bool, OpenAlexError> {
let url = format!("{}/works?per_page=1", self.base_url);
let response = self.client.get(&url).send().await?;
Ok(response.status().is_success())
}
/// Fetch a page of works with pagination
pub async fn fetch_works_page(
&self,
filter: &str,
cursor: Option<String>,
per_page: usize,
) -> Result<(Vec<Work>, Option<String>), OpenAlexError> {
let mut params = format!("per_page={}", per_page);
if !filter.is_empty() {
params.push_str(&format!("&{}", filter));
}
if let Some(c) = cursor {
params.push_str(&format!("&cursor={}", c));
} else {
// Use cursor-based pagination for bulk
params.push_str("&cursor=*");
}
let url = self.build_url("works", &params);
let response = self.client.get(&url).send().await?;
match response.status() {
StatusCode::OK => {
let api_response: ApiResponse<Work> = response.json().await?;
Ok((api_response.results, api_response.meta.next_cursor))
}
StatusCode::TOO_MANY_REQUESTS => {
let retry_after = response
.headers()
.get("retry-after")
.and_then(|v| v.to_str().ok())
.and_then(|s| s.parse().ok())
.unwrap_or(60);
Err(OpenAlexError::RateLimited(retry_after))
}
status => Err(OpenAlexError::Api(format!(
"Unexpected status: {}",
status
))),
}
}
/// Fetch a single work by ID
pub async fn get_work(&self, id: &str) -> Result<Work, OpenAlexError> {
// Normalize ID format
let normalized_id = if id.starts_with("https://") {
id.to_string()
} else if id.starts_with("W") {
format!("https://openalex.org/{}", id)
} else {
return Err(OpenAlexError::InvalidId(id.to_string()));
};
let url = self.build_url(&format!("works/{}", normalized_id), "");
let response = self.client.get(&url).send().await?;
match response.status() {
StatusCode::OK => Ok(response.json().await?),
StatusCode::NOT_FOUND => Err(OpenAlexError::InvalidId(id.to_string())),
status => Err(OpenAlexError::Api(format!(
"Unexpected status: {}",
status
))),
}
}
/// Search works by query
pub async fn search_works(
&self,
query: &str,
per_page: usize,
) -> Result<Vec<Work>, OpenAlexError> {
let params = format!("search={}&per_page={}", urlencoding::encode(query), per_page);
let url = self.build_url("works", &params);
let response = self.client.get(&url).send().await?;
match response.status() {
StatusCode::OK => {
let api_response: ApiResponse<Work> = response.json().await?;
Ok(api_response.results)
}
status => Err(OpenAlexError::Api(format!(
"Unexpected status: {}",
status
))),
}
}
/// Fetch works by topic
pub async fn works_by_topic(
&self,
topic_id: &str,
per_page: usize,
) -> Result<Vec<Work>, OpenAlexError> {
let filter = format!("filter=primary_topic.id:{}", topic_id);
let (works, _) = self.fetch_works_page(&filter, None, per_page).await?;
Ok(works)
}
/// Fetch works by author
pub async fn works_by_author(
&self,
author_id: &str,
per_page: usize,
) -> Result<Vec<Work>, OpenAlexError> {
let filter = format!("filter=authorships.author.id:{}", author_id);
let (works, _) = self.fetch_works_page(&filter, None, per_page).await?;
Ok(works)
}
/// Fetch works by institution
pub async fn works_by_institution(
&self,
institution_id: &str,
per_page: usize,
) -> Result<Vec<Work>, OpenAlexError> {
let filter = format!(
"filter=authorships.institutions.id:{}",
institution_id
);
let (works, _) = self.fetch_works_page(&filter, None, per_page).await?;
Ok(works)
}
/// Fetch works citing a specific work
pub async fn citing_works(
&self,
work_id: &str,
per_page: usize,
) -> Result<Vec<Work>, OpenAlexError> {
let filter = format!("filter=cites:{}", work_id);
let (works, _) = self.fetch_works_page(&filter, None, per_page).await?;
Ok(works)
}
/// Fetch works cited by a specific work
pub async fn cited_by_work(&self, work_id: &str) -> Result<Vec<Work>, OpenAlexError> {
let work = self.get_work(work_id).await?;
// Fetch referenced works
let mut cited_works = Vec::new();
for ref_id in work.referenced_works.iter().take(100) {
// Limit to avoid too many requests
if let Ok(cited) = self.get_work(ref_id).await {
cited_works.push(cited);
}
}
Ok(cited_works)
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_client_creation() {
let client = OpenAlexClient::new(None);
assert_eq!(client.base_url, "https://api.openalex.org");
}
#[test]
fn test_client_with_email() {
let client = OpenAlexClient::new(Some("test@example.com".to_string()));
let url = client.build_url("works", "per_page=10");
assert!(url.contains("mailto=test@example.com"));
}
#[test]
fn test_url_building() {
let client = OpenAlexClient::new(None);
let url = client.build_url("works", "filter=publication_year:2023");
assert!(url.starts_with("https://api.openalex.org/works"));
assert!(url.contains("filter=publication_year:2023"));
}
}