stemedb/crates/stemedb-query/tests/battery/battery1_semaglutide.rs

//! Battery 1: The Semaglutide Scenario.
//!
//! Validates the exact scenario from `what-is-episteme.md`:
//! four sources, four tiers, one subject, conflicting claims.
//!
//! # Test Coverage
//!
//! | Test | Pipeline Stage | Validates |
//! |------|---------------|-----------|
//! | `test_semaglutide_four_sources_ingest_and_query` | Full pipeline | Multi-lens resolution |
//! | `test_semaglutide_skeptic_analysis` | Skeptic | Conflict landscape grouping |
//! | `test_semaglutide_source_class_decay` | Decay | Tier-specific confidence decay |
//! | `test_semaglutide_time_travel` | Query | as_of temporal filtering |

#![allow(clippy::expect_used)] // Test code uses expect() for clear failure messages

use super::helpers::*;

/// Test 1.1: Full pipeline with 4 sources, verified through multiple lenses.
///
/// Setup:
/// - Agent A: FDA regulatory warning (Tier 0, confidence 1.0)
/// - Agent B: Clinical trial no-signal (Tier 1, confidence 0.9)
/// - Agent C: Patient report gastroparesis (Tier 5, confidence 0.2)
/// - Agent D: Another clinical no-signal (Tier 1, confidence 0.9)
///
/// Proves:
/// 1. Raw query returns all 4 assertions
/// 2. TrustAwareAuthority picks Regulatory (highest confidence * default trust)
/// 3. RecencyLens picks Agent D (most recent timestamp)
/// 4. All 4 assertions persist in store
#[tokio::test]
async fn test_semaglutide_four_sources_ingest_and_query() {
    let dir = tempdir().expect("create temp dir");
    let wal_dir = dir.path().join("wal");
    let db_dir = dir.path().join("db");

    let base_ts: u64 = 1_000_000;

    // === Setup: Create 4 conflicting assertions ===

    // Agent A: FDA regulatory warning (Tier 0, confidence 1.0)
    let agent_a = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("gastroparesis_warning".to_string()),
        SourceClass::Regulatory,
        1.0,
        base_ts,
    );

    // Agent B: Clinical trial - no signal (Tier 1, confidence 0.9)
    let agent_b = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("no_gastroparesis_signal".to_string()),
        SourceClass::Clinical,
        0.9,
        base_ts + 1,
    );

    // Agent C: Patient report - gastroparesis (Tier 5, confidence 0.2)
    let agent_c = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("gastroparesis".to_string()),
        SourceClass::Anecdotal,
        0.2,
        base_ts + 2,
    );

    // Agent D: Another clinical trial - no signal (Tier 1, confidence 0.9)
    let agent_d = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("no_gastroparesis_signal".to_string()),
        SourceClass::Clinical,
        0.9,
        base_ts + 3,
    );

    // === Step 1: Write all 4 to WAL ===
    let mut journal = Journal::open(&wal_dir).expect("open journal");
    journal.append(serialize_assertion(&agent_a).expect("ser")).expect("append a");
    journal.append(serialize_assertion(&agent_b).expect("ser")).expect("append b");
    journal.append(serialize_assertion(&agent_c).expect("ser")).expect("append c");
    journal.append(serialize_assertion(&agent_d).expect("ser")).expect("append d");

    // === Step 2: Ingest all 4 via IngestWorker ===
    let journal = Arc::new(Mutex::new(journal));
    let store = Arc::new(HybridStore::open(&db_dir).expect("open store"));

    let mut worker =
        IngestWorker::new(journal.clone(), store.clone()).await.expect("create worker");

    for _ in 0..4 {
        let bytes = worker.step().await.expect("ingest step");
        assert!(bytes > 0, "should process data from WAL");
    }

    // Verify H: keys exist (subject-prefixed: Semaglutide\x00H:{hash})
    let h_prefix = key_codec::assertion_key("Semaglutide", "");
    let h_entries = store.scan_prefix(&h_prefix).await.expect("scan H:");
    assert_eq!(h_entries.len(), 4, "should have 4 assertions stored");

    // Verify SP: index created (subject-prefixed: Semaglutide\x00SP:{predicate})
    let sp_prefix = key_codec::subject_predicate_scan_prefix("Semaglutide");
    let sp_entries = store.scan_prefix(&sp_prefix).await.expect("scan SP:");
    assert_eq!(sp_entries.len(), 1, "should have one SP: index entry");

    // === Assert 1: Raw query (no materialization) returns all 4 ===
    let engine = QueryEngine::new(store.clone());
    let query = Query::builder().subject("Semaglutide").predicate("has_side_effect").build();

    let result = engine.execute(&query).await.expect("raw query");
    assert_eq!(result.assertions.len(), 4, "raw query should return all 4 assertions");

    // === Assert 2: TrustAwareAuthority picks Regulatory (Agent A) ===
    // With default trust (0.5 for all agents):
    //   Agent A: 1.0 * 0.5 = 0.50 (winner)
    //   Agent B: 0.9 * 0.5 = 0.45
    //   Agent C: 0.2 * 0.5 = 0.10
    //   Agent D: 0.9 * 0.5 = 0.45
    let trust_store = Arc::new(GenericTrustRankStore::new(store.clone()));
    let authority_lens = TrustAwareAuthorityLens::new(trust_store);
    let materializer = Materializer::new(store.clone(), Box::new(authority_lens));

    let report = materializer.step().await.expect("materialize authority");
    assert_eq!(report.views_updated, 1, "should update one view");

    let authority_result = engine.execute(&query).await.expect("authority query");
    assert_eq!(authority_result.assertions.len(), 1, "materialized query returns winner");
    assert_eq!(
        authority_result.assertions[0].object,
        ObjectValue::Text("gastroparesis_warning".to_string()),
        "Authority lens should pick Regulatory assertion (highest confidence * default trust)"
    );

    // === Assert 3: RecencyLens picks Agent D (most recent timestamp) ===
    let recency_lens = SyncLensWrapper(RecencyLens);
    let materializer2 = Materializer::new(store.clone(), Box::new(recency_lens));

    let report2 = materializer2.step().await.expect("materialize recency");
    assert_eq!(report2.views_updated, 1, "should update view with recency winner");

    let recency_result = engine.execute(&query).await.expect("recency query");
    assert_eq!(recency_result.assertions.len(), 1, "materialized query returns winner");
    assert_eq!(
        recency_result.assertions[0].object,
        ObjectValue::Text("no_gastroparesis_signal".to_string()),
        "Recency lens should pick Agent D (most recent timestamp)"
    );
    assert_eq!(
        recency_result.assertions[0].timestamp,
        base_ts + 3,
        "Winner should have the latest timestamp"
    );

    // === Assert 4: All 4 assertions still persist in store ===
    let all_h = store.scan_prefix(&h_prefix).await.expect("final scan H:");
    assert_eq!(all_h.len(), 4, "all 4 assertions should persist in store");
}

/// Test 1.2: Skeptic analysis surfaces the conflict landscape.
///
/// With 4 assertions across 3 distinct object values:
/// - "gastroparesis_warning" (1 assertion, Regulatory)
/// - "no_gastroparesis_signal" (2 assertions, Clinical)
/// - "gastroparesis" (1 assertion, Anecdotal)
///
/// Proves the Skeptic lens correctly groups claims, counts assertions,
/// and identifies the conflict as Contested.
#[tokio::test]
async fn test_semaglutide_skeptic_analysis() {
    let store = Arc::new(HybridStore::open_temp().expect("store"));
    let index_store = GenericIndexStore::new(store.clone());

    let base_ts: u64 = 1_000_000;

    // === Setup: Store 4 assertions directly ===

    let agent_a = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("gastroparesis_warning")
        .source_class(SourceClass::Regulatory)
        .confidence(1.0)
        .agent_id([1u8; 32])
        .timestamp(base_ts)
        .build();

    let agent_b = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("no_gastroparesis_signal")
        .source_class(SourceClass::Clinical)
        .confidence(0.9)
        .agent_id([2u8; 32])
        .timestamp(base_ts + 1)
        .build();

    let agent_c = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("gastroparesis")
        .source_class(SourceClass::Anecdotal)
        .confidence(0.2)
        .agent_id([3u8; 32])
        .timestamp(base_ts + 2)
        .build();

    let agent_d = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("no_gastroparesis_signal")
        .source_class(SourceClass::Clinical)
        .confidence(0.9)
        .agent_id([4u8; 32])
        .timestamp(base_ts + 3)
        .build();

    store_assertion_direct(&store, &index_store, &agent_a).await;
    store_assertion_direct(&store, &index_store, &agent_b).await;
    store_assertion_direct(&store, &index_store, &agent_c).await;
    store_assertion_direct(&store, &index_store, &agent_d).await;

    // === Run SkepticResolver ===
    let vote_store = Arc::new(GenericVoteStore::new(store.clone()));
    let trust_store = Arc::new(GenericTrustRankStore::new(store.clone()));
    let resolver = SkepticResolver::new(store.clone(), vote_store, trust_store);

    let result = resolver.resolve("Semaglutide", "has_side_effect").await.expect("resolve");
    let view = result.expect("should have a SkepticView");
    let analysis = &view.analysis;

    // === Asserts ===

    // Total candidates
    assert_eq!(analysis.candidates_count, 4, "should consider all 4 assertions");

    // 3 distinct groups: "gastroparesis_warning" (1), "no_gastroparesis_signal" (2), "gastroparesis" (1)
    assert_eq!(analysis.claims.len(), 3, "should have 3 distinct claim groups");

    // Status should be Contested (significant disagreement across 3 groups)
    assert_eq!(
        analysis.status,
        ResolutionStatus::Contested,
        "4 assertions across 3 groups should be contested"
    );

    // Conflict score should be meaningful (Shannon entropy of 3-way split)
    assert!(
        analysis.conflict_score > 0.3,
        "conflict score {} should be > 0.3 for 3-way split",
        analysis.conflict_score
    );

    // Find the "no_gastroparesis_signal" group - should have 2 assertions
    let no_signal_claim = analysis
        .claims
        .iter()
        .find(|c| matches!(&c.value, ObjectValue::Text(t) if t == "no_gastroparesis_signal"))
        .expect("should have no_gastroparesis_signal claim");
    assert_eq!(
        no_signal_claim.assertion_count, 2,
        "no_gastroparesis_signal should have 2 supporting assertions"
    );

    // Claims should be sorted descending by weight_share
    for window in analysis.claims.windows(2) {
        assert!(
            window[0].weight_share >= window[1].weight_share,
            "claims should be sorted descending by weight_share: {} >= {}",
            window[0].weight_share,
            window[1].weight_share
        );
    }
}

/// Test 1.3: Source-class-aware decay at 180 days.
///
/// With all 4 assertions timestamped 180 days ago:
/// - Regulatory (Tier 0): No decay, confidence stays 1.0
/// - Clinical (Tier 1, 730-day half-life): 0.9 * 2^(-180/730) ~ 0.759
/// - Anecdotal (Tier 5, 30-day half-life): 0.2 * 2^(-6) ~ 0.003
///
/// After decay, Authority lens with default trust still picks Regulatory.
#[tokio::test]
async fn test_semaglutide_source_class_decay() {
    let now: u64 = 1_000_000_000;
    let days_180: u64 = 180 * 86_400;
    let past = now - days_180;

    // All assertions at 180 days ago
    let regulatory = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("gastroparesis_warning")
        .source_class(SourceClass::Regulatory)
        .confidence(1.0)
        .agent_id([1u8; 32])
        .timestamp(past)
        .build();

    let clinical_b = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("no_gastroparesis_signal")
        .source_class(SourceClass::Clinical)
        .confidence(0.9)
        .agent_id([2u8; 32])
        .timestamp(past)
        .build();

    let anecdotal = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("gastroparesis")
        .source_class(SourceClass::Anecdotal)
        .confidence(0.2)
        .agent_id([3u8; 32])
        .timestamp(past)
        .build();

    let clinical_d = AssertionBuilder::new()
        .subject("Semaglutide")
        .predicate("has_side_effect")
        .object_text("no_gastroparesis_signal")
        .source_class(SourceClass::Clinical)
        .confidence(0.9)
        .agent_id([4u8; 32])
        .timestamp(past)
        .build();

    let assertions = vec![regulatory, clinical_b, anecdotal, clinical_d];

    // Apply tier-specific decay
    let fallback_halflife: u64 = 365 * 86_400; // 1 year fallback
    let decayed = apply_source_class_decay(&assertions, fallback_halflife, now);

    assert_eq!(decayed.len(), 4);

    // Regulatory (Tier 0): No decay, stays at 1.0
    assert_eq!(decayed[0].confidence, 1.0, "Regulatory should not decay");

    // Clinical (Tier 1, 730-day half-life): 0.9 * 2^(-180/730) ~ 0.759
    let clinical_conf = decayed[1].confidence;
    assert!(
        clinical_conf > 0.7 && clinical_conf < 0.85,
        "Clinical should decay to ~0.759, got {}",
        clinical_conf
    );

    // Anecdotal (Tier 5, 30-day half-life): 0.2 * 2^(-180/30) = 0.2 * 2^(-6) ~ 0.003
    let anecdotal_conf = decayed[2].confidence;
    assert!(anecdotal_conf < 0.01, "Anecdotal should decay to near zero, got {}", anecdotal_conf);

    // Second clinical should match first clinical's decay
    let clinical2_conf = decayed[3].confidence;
    assert!(
        (clinical2_conf - clinical_conf).abs() < 0.001,
        "Both clinical assertions should decay identically: {} vs {}",
        clinical_conf,
        clinical2_conf
    );

    // After decay, Authority lens with default trust still picks Regulatory
    // Weighted scores (default trust 0.5):
    //   Regulatory: 1.0 * 0.5 = 0.50
    //   Clinical:   ~0.759 * 0.5 = ~0.38
    //   Anecdotal:  ~0.003 * 0.5 = ~0.001
    let store = HybridStore::open_temp().expect("store");
    let trust_store = Arc::new(GenericTrustRankStore::new(store));
    let lens = TrustAwareAuthorityLens::new(trust_store);

    let resolution = lens.resolve_async(&decayed).await;

    assert!(resolution.winner.is_some(), "should have a winner");
    assert_eq!(
        resolution.winner.as_ref().expect("winner").object,
        ObjectValue::Text("gastroparesis_warning".to_string()),
        "After decay, Regulatory assertion should still win with Authority lens"
    );
}

/// Test 1.4: Time-travel query filters by timestamp.
///
/// With 4 assertions at timestamps 1000, 1100, 1200, 1300:
/// - Query with `as_of: 1150` returns only assertions at T=1000 and T=1100
/// - Assertions at T=1200 and T=1300 are excluded
/// - The conflict landscape is reduced to a 2-way split
#[tokio::test]
async fn test_semaglutide_time_travel() {
    let dir = tempdir().expect("create temp dir");
    let wal_dir = dir.path().join("wal");
    let db_dir = dir.path().join("db");

    // Agent A: T=1000 (Regulatory)
    let agent_a = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("gastroparesis_warning".to_string()),
        SourceClass::Regulatory,
        1.0,
        1000,
    );

    // Agent B: T=1100 (Clinical)
    let agent_b = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("no_gastroparesis_signal".to_string()),
        SourceClass::Clinical,
        0.9,
        1100,
    );

    // Agent C: T=1200 (Anecdotal)
    let agent_c = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("gastroparesis".to_string()),
        SourceClass::Anecdotal,
        0.2,
        1200,
    );

    // Agent D: T=1300 (Clinical)
    let agent_d = create_signed_assertion_with_source(
        "Semaglutide",
        "has_side_effect",
        ObjectValue::Text("no_gastroparesis_signal".to_string()),
        SourceClass::Clinical,
        0.9,
        1300,
    );

    // === Write to WAL and ingest ===
    let mut journal = Journal::open(&wal_dir).expect("open journal");
    journal.append(serialize_assertion(&agent_a).expect("ser")).expect("append a");
    journal.append(serialize_assertion(&agent_b).expect("ser")).expect("append b");
    journal.append(serialize_assertion(&agent_c).expect("ser")).expect("append c");
    journal.append(serialize_assertion(&agent_d).expect("ser")).expect("append d");

    let journal = Arc::new(Mutex::new(journal));
    let store = Arc::new(HybridStore::open(&db_dir).expect("open store"));

    let mut worker =
        IngestWorker::new(journal.clone(), store.clone()).await.expect("create worker");

    for _ in 0..4 {
        let bytes = worker.step().await.expect("ingest step");
        assert!(bytes > 0, "should process data from WAL");
    }

    // Verify all 4 ingested (subject-prefixed: Semaglutide\x00H:{hash})
    let h_prefix = key_codec::assertion_key("Semaglutide", "");
    let h_entries = store.scan_prefix(&h_prefix).await.expect("scan H:");
    assert_eq!(h_entries.len(), 4, "should have 4 assertions stored");

    // === Query with as_of: 1150 (between B at 1100 and C at 1200) ===
    let engine = QueryEngine::new(store.clone());
    let query =
        Query::builder().subject("Semaglutide").predicate("has_side_effect").as_of(1150).build();

    let result = engine.execute(&query).await.expect("time-travel query");

    // Only 2 assertions should pass the timestamp filter
    assert_eq!(
        result.assertions.len(),
        2,
        "as_of=1150 should return only A (T=1000) and B (T=1100), got {}",
        result.assertions.len()
    );

    // Verify the correct assertions are returned
    let timestamps: Vec<u64> = result.assertions.iter().map(|a| a.timestamp).collect();
    assert!(timestamps.contains(&1000), "should include Agent A (T=1000)");
    assert!(timestamps.contains(&1100), "should include Agent B (T=1100)");

    // Verify the excluded assertions are NOT returned
    assert!(!timestamps.contains(&1200), "should exclude Agent C (T=1200)");
    assert!(!timestamps.contains(&1300), "should exclude Agent D (T=1300)");

    // The conflict landscape is now a 2-way split (regulatory vs clinical)
    let objects: Vec<&ObjectValue> = result.assertions.iter().map(|a| &a.object).collect();
    assert!(
        objects.contains(&&ObjectValue::Text("gastroparesis_warning".to_string())),
        "should include regulatory warning"
    );
    assert!(
        objects.contains(&&ObjectValue::Text("no_gastroparesis_signal".to_string())),
        "should include clinical no-signal"
    );
}