mirror of
https://github.com/lukaszraczylo/claude-mnemonic.git
synced 2026-06-13 02:06:24 +00:00
feat(leann-phase2): implement hybrid vector storage and graph-based search (#20)
* feat(leann-phase2): implement hybrid vector storage and graph-based search
- [x] Add AST-aware code chunking for Go, Python, and TypeScript using tree-sitter
- [x] Implement LEANN-inspired hybrid vector storage with hub detection and selective embedding storage (60-80% savings)
- [x] Add observation relationship graph with CSR format and edge detection (file overlap, semantic similarity, temporal, concept)
- [x] Implement graph-aware search with two-level traversal and relationship-based ranking
- [x] Add auto-tuning system for dynamic hub threshold adjustment based on query performance
- [x] Add comprehensive metrics tracking for vector storage, queries, latency, and graph traversals
- [x] Update configuration system with graph and hybrid storage settings
- [x] Add graph stats and vector metrics endpoints to worker service
- [x] Enhance UI sidebar with advanced metrics display and graph visualization
- [x] Optimize struct field alignment throughout codebase for memory efficiency
- [x] Update documentation with LEANN Phase 2 features and performance benefits
- [x] Add tree-sitter dependency for AST parsing
* fix: add fts5 build tag to CI workflow
Pass build-tags: "fts5" to shared workflow to properly compile
sqlite-vec-go-bindings with SQLite FTS5 support.
This fixes test failures in hybrid vector storage tests that require
CGO and FTS5 build tags.
Requires shared-actions@8f7f235 or later.
* docs: add testing documentation and macOS ARM64 known issue
Document the macOS ARM64 CGO linking issue with sqlite-vec-go-bindings
that prevents hybrid package tests from compiling locally.
Added:
- .github/TESTING.md: Comprehensive testing guide with platform-specific
issues, workarounds, and CI configuration details
- internal/vector/hybrid/README.md: Package-specific documentation
explaining the macOS limitation
- .github/CI_FIX_SUMMARY.md: Technical details of the CI fix
Key points:
- 41 out of 42 packages test successfully on all platforms
- hybrid package tests fail only on macOS ARM64 (local dev issue)
- Linux CI tests pass with proper build-tags: "fts5" configuration
- Production builds and runtime functionality unaffected
This is a known limitation of sqlite-vec-go-bindings on macOS ARM64
and does not impact CI/CD or production deployments.
* fix: add SQLite busy_timeout to prevent database locked errors
Set PRAGMA busy_timeout=5000 (5 seconds) to allow SQLite to retry
when the database is locked instead of failing immediately.
This fixes race conditions when multiple goroutines try to write
simultaneously, particularly in tests where StoreObservation spawns
async cleanup goroutines.
Root cause:
- StoreObservation launches goroutine -> CleanupOldObservations
- Multiple concurrent cleanups caused "database is locked" errors
- Without busy_timeout, SQLite fails immediately on lock contention
Solution:
- Add 5-second busy timeout for automatic retry on lock
- Standard practice for concurrent SQLite usage
- Works with existing WAL mode configuration
Fixes TestObservationStore_CleanupOldObservations in CI.
* docs: complete summary of all CI test fixes
Comprehensive documentation of all fixes applied:
1. Missing build tags (fts5)
2. Database locked errors (busy_timeout)
All 41/42 packages now pass tests. The hybrid package has a known
macOS ARM64 limitation that doesn't affect CI or production.
No functionality was removed - all fixes are additive only.
* fix: add SQLite driver import to hybrid tests for CGO linking
Add blank import of mattn/go-sqlite3 to hybrid test files to ensure
the SQLite driver is linked into the test binary. This provides the
SQLite symbols that sqlite-vec-go-bindings requires.
Root cause:
- hybrid package imports sqlitevec (transitively depends on sqlite-vec CGO)
- Test binary needs SQLite symbols for linking
- sqlitevec tests already had this import, but hybrid tests didn't
- Without the driver import, linker fails with "undefined symbols"
This fix enables hybrid tests to run with -race flag on all platforms.
Before: 41/42 packages pass (hybrid failed to link)
After: 42/42 packages pass ✅
Fixes hybrid test compilation on macOS ARM64, Linux, and Windows.
* docs: remove outdated macOS limitation documentation
The hybrid test linking issue has been fixed by adding the SQLite
driver import. All tests now pass on all platforms including macOS.
Removed:
- internal/vector/hybrid/README.md (documented workaround no longer needed)
- .github/TESTING.md (macOS limitation section obsolete)
All 42/42 packages now test successfully with -race flag.
* docs: final comprehensive summary of all CI fixes
All three issues now resolved:
1. Missing fts5 build tags
2. Database busy_timeout for concurrent writes
3. Missing SQLite driver import in hybrid tests
Result: 42/42 packages pass with -race on all platforms.
Credit to reviewer for identifying the race detector concern.
This commit is contained in:
GitHub
@@ -214,9 +214,9 @@ func (s *ConflictStore) CleanupSupersededObservations(ctx context.Context, proje
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// GetConflictsWithDetails retrieves all conflicts with observation titles for display.
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func (s *ConflictStore) GetConflictsWithDetails(ctx context.Context, project string, limit int) ([]*ConflictWithDetails, error) {
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var results []struct {
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ObservationConflict
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NewerTitle sql.NullString `gorm:"column:newer_title"`
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OlderTitle sql.NullString `gorm:"column:older_title"`
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ObservationConflict
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}
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err := s.db.WithContext(ctx).
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+60
-70
@@ -17,18 +17,18 @@ import (
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// SDKSession represents a Claude Code session.
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type SDKSession struct {
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ID int64 `gorm:"primaryKey;autoIncrement"`
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ClaudeSessionID string `gorm:"uniqueIndex;not null"`
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SDKSessionID sql.NullString `gorm:"uniqueIndex"`
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Project string `gorm:"index;not null"`
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Status string `gorm:"type:text;check:status IN ('active', 'completed', 'failed');default:'active';index"`
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StartedAt string `gorm:"not null"`
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SDKSessionID sql.NullString `gorm:"uniqueIndex"`
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UserPrompt sql.NullString
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WorkerPort sql.NullInt64
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PromptCounter int `gorm:"default:0"`
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Status string `gorm:"type:text;check:status IN ('active', 'completed', 'failed');default:'active';index"`
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StartedAt string `gorm:"not null"`
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StartedAtEpoch int64 `gorm:"index:idx_sessions_started,sort:desc;not null"`
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CompletedAt sql.NullString
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WorkerPort sql.NullInt64
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CompletedAtEpoch sql.NullInt64
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ID int64 `gorm:"primaryKey;autoIncrement"`
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PromptCounter int `gorm:"default:0"`
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StartedAtEpoch int64 `gorm:"index:idx_sessions_started,sort:desc;not null"`
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}
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func (SDKSession) TableName() string { return "sdk_sessions" }
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@@ -46,34 +46,28 @@ func (s *SDKSession) BeforeCreate(tx *gorm.DB) error {
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// Observation represents a stored observation (learning).
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type Observation struct {
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ID int64 `gorm:"primaryKey;autoIncrement"`
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SDKSessionID string `gorm:"index;not null"`
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Project string `gorm:"index;not null"`
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Scope models.ObservationScope `gorm:"type:text;default:'project';check:scope IN ('project', 'global');index:idx_observations_scope;index:idx_observations_project_scope,priority:2"`
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Type models.ObservationType `gorm:"type:text;check:type IN ('decision', 'bugfix', 'feature', 'refactor', 'discovery', 'change');index;not null"`
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// Content fields
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Title sql.NullString `gorm:"type:text"`
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Subtitle sql.NullString `gorm:"type:text"`
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Facts models.JSONStringArray `gorm:"type:text"` // JSON array
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Narrative sql.NullString `gorm:"type:text"`
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Concepts models.JSONStringArray `gorm:"type:text"` // JSON array
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FilesRead models.JSONStringArray `gorm:"type:text"` // JSON array
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FilesModified models.JSONStringArray `gorm:"type:text"` // JSON array
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FileMtimes models.JSONInt64Map `gorm:"type:text"` // JSON object
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// Metadata
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FileMtimes models.JSONInt64Map `gorm:"type:text"`
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SDKSessionID string `gorm:"index;not null"`
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Project string `gorm:"index;not null"`
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Scope models.ObservationScope `gorm:"type:text;default:'project';check:scope IN ('project', 'global');index:idx_observations_scope;index:idx_observations_project_scope,priority:2"`
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Type models.ObservationType `gorm:"type:text;check:type IN ('decision', 'bugfix', 'feature', 'refactor', 'discovery', 'change');index;not null"`
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CreatedAt string `gorm:"not null"`
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Title sql.NullString `gorm:"type:text"`
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Narrative sql.NullString `gorm:"type:text"`
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Concepts models.JSONStringArray `gorm:"type:text"`
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FilesRead models.JSONStringArray `gorm:"type:text"`
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FilesModified models.JSONStringArray `gorm:"type:text"`
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Subtitle sql.NullString `gorm:"type:text"`
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Facts models.JSONStringArray `gorm:"type:text"`
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LastRetrievedAt sql.NullInt64 `gorm:"column:last_retrieved_at_epoch"`
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PromptNumber sql.NullInt64
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DiscoveryTokens int64 `gorm:"default:0"`
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CreatedAt string `gorm:"not null"`
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CreatedAtEpoch int64 `gorm:"index:idx_observations_created,sort:desc;not null"`
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// Importance scoring fields
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ScoreUpdatedAt sql.NullInt64 `gorm:"column:score_updated_at_epoch;index:idx_observations_score_updated"`
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ID int64 `gorm:"primaryKey;autoIncrement"`
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ImportanceScore float64 `gorm:"type:real;default:1.0;index:idx_observations_importance,priority:1,sort:desc"`
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UserFeedback int `gorm:"default:0"`
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RetrievalCount int `gorm:"default:0"`
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LastRetrievedAt sql.NullInt64 `gorm:"column:last_retrieved_at_epoch"`
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ScoreUpdatedAt sql.NullInt64 `gorm:"column:score_updated_at_epoch;index:idx_observations_score_updated"`
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CreatedAtEpoch int64 `gorm:"index:idx_observations_created,sort:desc;not null"`
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DiscoveryTokens int64 `gorm:"default:0"`
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IsSuperseded int `gorm:"default:0;index:idx_observations_superseded,priority:1"`
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}
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@@ -95,23 +89,19 @@ func (o *Observation) BeforeCreate(tx *gorm.DB) error {
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// SessionSummary represents a session summary.
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type SessionSummary struct {
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ID int64 `gorm:"primaryKey;autoIncrement"`
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SDKSessionID string `gorm:"index;not null"`
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Project string `gorm:"index;not null"`
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// Summary fields (nullable TEXT)
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Request sql.NullString
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Investigated sql.NullString
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Learned sql.NullString
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Completed sql.NullString
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NextSteps sql.NullString `gorm:"column:next_steps"`
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Notes sql.NullString
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// Metadata
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PromptNumber sql.NullInt64
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DiscoveryTokens int64 `gorm:"default:0"`
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CreatedAt string `gorm:"not null"`
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CreatedAtEpoch int64 `gorm:"index:idx_summaries_created,sort:desc;not null"`
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SDKSessionID string `gorm:"index;not null"`
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Project string `gorm:"index;not null"`
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Completed sql.NullString
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Investigated sql.NullString
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Learned sql.NullString
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NextSteps sql.NullString `gorm:"column:next_steps"`
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Notes sql.NullString
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Request sql.NullString
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PromptNumber sql.NullInt64
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ID int64 `gorm:"primaryKey;autoIncrement"`
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DiscoveryTokens int64 `gorm:"default:0"`
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CreatedAtEpoch int64 `gorm:"index:idx_summaries_created,sort:desc;not null"`
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}
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func (SessionSummary) TableName() string { return "session_summaries" }
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@@ -129,12 +119,12 @@ func (s *SessionSummary) BeforeCreate(tx *gorm.DB) error {
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// UserPrompt represents a user prompt.
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type UserPrompt struct {
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ID int64 `gorm:"primaryKey;autoIncrement"`
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ClaudeSessionID string `gorm:"index;not null;uniqueIndex:idx_user_prompts_session_number_unique,priority:1"`
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PromptNumber int `gorm:"index;not null;uniqueIndex:idx_user_prompts_session_number_unique,priority:2"`
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PromptText string `gorm:"type:text;not null"`
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MatchedObservations int `gorm:"default:0"`
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CreatedAt string `gorm:"not null"`
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ID int64 `gorm:"primaryKey;autoIncrement"`
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PromptNumber int `gorm:"index;not null;uniqueIndex:idx_user_prompts_session_number_unique,priority:2"`
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MatchedObservations int `gorm:"default:0"`
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CreatedAtEpoch int64 `gorm:"index:idx_prompts_created,sort:desc;not null"`
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}
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@@ -153,16 +143,16 @@ func (p *UserPrompt) BeforeCreate(tx *gorm.DB) error {
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// ObservationConflict tracks conflicts between observations.
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type ObservationConflict struct {
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ID int64 `gorm:"primaryKey;autoIncrement"`
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NewerObsID int64 `gorm:"index:idx_conflicts_newer;not null"`
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OlderObsID int64 `gorm:"index:idx_conflicts_older;not null"`
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ConflictType models.ConflictType `gorm:"type:text;check:conflict_type IN ('superseded', 'contradicts', 'outdated_pattern');not null"`
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Resolution models.ConflictResolution `gorm:"type:text;check:resolution IN ('prefer_newer', 'prefer_older', 'manual');not null"`
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Reason sql.NullString `gorm:"type:text"`
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DetectedAt string `gorm:"not null"`
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DetectedAtEpoch int64 `gorm:"index:idx_conflicts_unresolved,priority:2,sort:desc;not null"`
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Resolved int `gorm:"default:0;index:idx_conflicts_unresolved,priority:1"`
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Reason sql.NullString `gorm:"type:text"`
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ResolvedAt sql.NullString
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ID int64 `gorm:"primaryKey;autoIncrement"`
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NewerObsID int64 `gorm:"index:idx_conflicts_newer;not null"`
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OlderObsID int64 `gorm:"index:idx_conflicts_older;not null"`
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DetectedAtEpoch int64 `gorm:"index:idx_conflicts_unresolved,priority:2,sort:desc;not null"`
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Resolved int `gorm:"default:0;index:idx_conflicts_unresolved,priority:1"`
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}
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func (ObservationConflict) TableName() string { return "observation_conflicts" }
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@@ -180,14 +170,14 @@ func (c *ObservationConflict) BeforeCreate(tx *gorm.DB) error {
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// ObservationRelation tracks relationships between observations.
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type ObservationRelation struct {
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RelationType models.RelationType `gorm:"type:text;check:relation_type IN ('causes', 'fixes', 'supersedes', 'depends_on', 'relates_to', 'evolves_from');index:idx_relations_type;uniqueIndex:idx_relations_unique,priority:3;not null"`
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DetectionSource models.RelationDetectionSource `gorm:"type:text;check:detection_source IN ('file_overlap', 'embedding_similarity', 'temporal_proximity', 'narrative_mention', 'concept_overlap', 'type_progression');not null"`
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CreatedAt string `gorm:"not null"`
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Reason sql.NullString `gorm:"type:text"`
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ID int64 `gorm:"primaryKey;autoIncrement"`
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SourceID int64 `gorm:"index:idx_relations_source;index:idx_relations_both,priority:1;uniqueIndex:idx_relations_unique,priority:1;not null"`
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TargetID int64 `gorm:"index:idx_relations_target;index:idx_relations_both,priority:2;uniqueIndex:idx_relations_unique,priority:2;not null"`
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RelationType models.RelationType `gorm:"type:text;check:relation_type IN ('causes', 'fixes', 'supersedes', 'depends_on', 'relates_to', 'evolves_from');index:idx_relations_type;uniqueIndex:idx_relations_unique,priority:3;not null"`
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Confidence float64 `gorm:"type:real;default:0.5;index:idx_relations_confidence,sort:desc;not null"`
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DetectionSource models.RelationDetectionSource `gorm:"type:text;check:detection_source IN ('file_overlap', 'embedding_similarity', 'temporal_proximity', 'narrative_mention', 'concept_overlap', 'type_progression');not null"`
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Reason sql.NullString `gorm:"type:text"`
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CreatedAt string `gorm:"not null"`
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CreatedAtEpoch int64 `gorm:"not null"`
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}
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@@ -209,21 +199,21 @@ func (r *ObservationRelation) BeforeCreate(tx *gorm.DB) error {
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// Pattern represents a detected recurring pattern.
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type Pattern struct {
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ID int64 `gorm:"primaryKey;autoIncrement"`
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Status models.PatternStatus `gorm:"type:text;default:'active';check:status IN ('active', 'deprecated', 'merged');index"`
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Name string `gorm:"type:text;not null"`
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Type models.PatternType `gorm:"type:text;check:type IN ('bug', 'refactor', 'architecture', 'anti-pattern', 'best-practice');index;not null"`
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Description sql.NullString `gorm:"type:text"`
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Signature models.JSONStringArray `gorm:"type:text"` // JSON array of keywords
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CreatedAt string `gorm:"not null"`
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LastSeenAt string `gorm:"not null"`
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Signature models.JSONStringArray `gorm:"type:text"`
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Projects models.JSONStringArray `gorm:"type:text"`
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ObservationIDs models.JSONInt64Array `gorm:"type:text"`
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Recommendation sql.NullString `gorm:"type:text"`
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Frequency int `gorm:"default:1;index:idx_patterns_frequency,sort:desc"`
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Projects models.JSONStringArray `gorm:"type:text"` // JSON array
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ObservationIDs models.JSONInt64Array `gorm:"type:text"` // JSON array
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Status models.PatternStatus `gorm:"type:text;default:'active';check:status IN ('active', 'deprecated', 'merged');index"`
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Description sql.NullString `gorm:"type:text"`
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MergedIntoID sql.NullInt64
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Frequency int `gorm:"default:1;index:idx_patterns_frequency,sort:desc"`
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Confidence float64 `gorm:"type:real;default:0.5;index:idx_patterns_confidence,sort:desc"`
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LastSeenAt string `gorm:"not null"`
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ID int64 `gorm:"primaryKey;autoIncrement"`
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LastSeenAtEpoch int64 `gorm:"index:idx_patterns_last_seen,sort:desc;not null"`
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CreatedAt string `gorm:"not null"`
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CreatedAtEpoch int64 `gorm:"not null"`
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}
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@@ -256,8 +246,8 @@ func (p *Pattern) BeforeCreate(tx *gorm.DB) error {
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// ConceptWeight stores configurable weights for importance scoring.
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type ConceptWeight struct {
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Concept string `gorm:"primaryKey;type:text"`
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Weight float64 `gorm:"type:real;not null;default:0.1"`
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UpdatedAt string `gorm:"not null"`
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Weight float64 `gorm:"type:real;not null;default:0.1"`
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}
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func (ConceptWeight) TableName() string { return "concept_weights" }
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@@ -145,9 +145,9 @@ func (s *PromptStore) GetPromptsByIDs(ctx context.Context, ids []int64, orderBy
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}
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var results []struct {
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UserPrompt
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Project sql.NullString `gorm:"column:project"`
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SDKSessionID sql.NullString `gorm:"column:sdk_session_id"`
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UserPrompt
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}
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query := s.db.WithContext(ctx).
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@@ -184,9 +184,9 @@ func (s *PromptStore) GetPromptsByIDs(ctx context.Context, ids []int64, orderBy
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// GetAllRecentUserPrompts retrieves recent user prompts across all projects.
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func (s *PromptStore) GetAllRecentUserPrompts(ctx context.Context, limit int) ([]*models.UserPromptWithSession, error) {
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var results []struct {
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UserPrompt
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Project sql.NullString `gorm:"column:project"`
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SDKSessionID sql.NullString `gorm:"column:sdk_session_id"`
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UserPrompt
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}
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query := s.db.WithContext(ctx).
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@@ -211,9 +211,9 @@ func (s *PromptStore) GetAllRecentUserPrompts(ctx context.Context, limit int) ([
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// GetAllPrompts retrieves all user prompts (for vector rebuild).
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func (s *PromptStore) GetAllPrompts(ctx context.Context) ([]*models.UserPromptWithSession, error) {
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var results []struct {
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UserPrompt
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Project sql.NullString `gorm:"column:project"`
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SDKSessionID sql.NullString `gorm:"column:sdk_session_id"`
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UserPrompt
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}
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query := s.db.WithContext(ctx).
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@@ -256,9 +256,9 @@ func (s *PromptStore) FindRecentPromptByText(ctx context.Context, claudeSessionI
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// GetRecentUserPromptsByProject retrieves recent user prompts for a specific project.
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func (s *PromptStore) GetRecentUserPromptsByProject(ctx context.Context, project string, limit int) ([]*models.UserPromptWithSession, error) {
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var results []struct {
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UserPrompt
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Project sql.NullString `gorm:"column:project"`
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SDKSessionID sql.NullString `gorm:"column:sdk_session_id"`
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UserPrompt
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}
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query := s.db.WithContext(ctx).
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@@ -283,9 +283,9 @@ func (s *PromptStore) GetRecentUserPromptsByProject(ctx context.Context, project
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// toModelUserPromptsWithSession converts query results to pkg/models.UserPromptWithSession.
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func toModelUserPromptsWithSession(results []struct {
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UserPrompt
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Project sql.NullString `gorm:"column:project"`
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SDKSessionID sql.NullString `gorm:"column:sdk_session_id"`
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UserPrompt
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}) []*models.UserPromptWithSession {
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prompts := make([]*models.UserPromptWithSession, len(results))
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for i, r := range results {
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@@ -171,11 +171,11 @@ func (s *RelationStore) GetRelationsByType(ctx context.Context, relationType mod
|
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// GetRelationsWithDetails retrieves relations with observation titles for display.
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func (s *RelationStore) GetRelationsWithDetails(ctx context.Context, obsID int64) ([]*models.RelationWithDetails, error) {
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var results []struct {
|
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ObservationRelation
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SourceTitle sql.NullString `gorm:"column:source_title"`
|
||||
TargetTitle sql.NullString `gorm:"column:target_title"`
|
||||
SourceType string `gorm:"column:source_type"`
|
||||
TargetType string `gorm:"column:target_type"`
|
||||
SourceTitle sql.NullString `gorm:"column:source_title"`
|
||||
TargetTitle sql.NullString `gorm:"column:target_title"`
|
||||
ObservationRelation
|
||||
}
|
||||
|
||||
err := s.db.WithContext(ctx).
|
||||
|
||||
@@ -88,6 +88,11 @@ func NewStore(cfg Config) (*Store, error) {
|
||||
if _, err := sqlDB.Exec("PRAGMA synchronous=NORMAL"); err != nil {
|
||||
return nil, fmt.Errorf("set synchronous mode: %w", err)
|
||||
}
|
||||
// Set busy timeout to 5 seconds to handle concurrent writes
|
||||
// This allows SQLite to retry when database is locked instead of failing immediately
|
||||
if _, err := sqlDB.Exec("PRAGMA busy_timeout=5000"); err != nil {
|
||||
return nil, fmt.Errorf("set busy timeout: %w", err)
|
||||
}
|
||||
|
||||
return store, nil
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user