feat: add PostgreSQL persistence layer with Neon DB support

internal/ontology/store_pg.go

@@ -0,0 +1,111 @@
+package ontology
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+
+	"github.com/jackc/pgx/v5/pgxpool"
+)
+
+type PostgresStore struct {
+	pool *pgxpool.Pool
+}
+
+func NewPostgresStore(pool *pgxpool.Pool) *PostgresStore {
+	return &PostgresStore{pool: pool}
+}
+
+func toJSON(v any) string {
+	b, _ := json.Marshal(v)
+	return string(b)
+}
+
+func (s *PostgresStore) Save(material Material, concepts []ConceptCandidate, edges []EdgeCandidate, gaps []Gap) error {
+	ctx := context.Background()
+	_, err := s.pool.Exec(ctx,
+		`INSERT INTO ontology_materials (id, title, source_type, body, created_at) VALUES ($1, $2, $3, $4, $5)`,
+		material.ID, material.Title, material.SourceType, material.Body, material.CreatedAt)
+	if err != nil {
+		return fmt.Errorf("insert material: %w", err)
+	}
+
+	for _, c := range concepts {
+		_, err := s.pool.Exec(ctx,
+			`INSERT INTO ontology_concepts (id, material_id, concept_id, concept_label, summary, review_state, evidence, created_at)
+			 VALUES ($1, $2, $3, $4, $5, $6, $7::jsonb, $8)`,
+			c.ID, material.ID, c.Concept.ID, c.Concept.Label, c.Summary, string(c.ReviewState),
+			toJSON(c.Evidence), c.CreatedAt)
+		if err != nil {
+			return fmt.Errorf("insert concept: %w", err)
+		}
+	}
+
+	for _, e := range edges {
+		_, err := s.pool.Exec(ctx,
+			`INSERT INTO ontology_edges (id, from_concept_id, to_concept_id, kind, evidence, created_at)
+			 VALUES ($1, $2, $3, $4, $5::jsonb, $6)`,
+			e.ID, e.From.ID, e.To.ID, string(e.Kind),
+			toJSON(e.Evidence), e.CreatedAt)
+		if err != nil {
+			return fmt.Errorf("insert edge: %w", err)
+		}
+	}
+
+	for _, g := range gaps {
+		_, err := s.pool.Exec(ctx,
+			`INSERT INTO ontology_gaps (id, concept_id, reason, evidence, created_at)
+			 VALUES ($1, $2, $3, $4::jsonb, $5)`,
+			g.ID, g.Concept.ID, g.Reason,
+			toJSON(g.SupportingEvidence), g.CreatedAt)
+		if err != nil {
+			return fmt.Errorf("insert gap: %w", err)
+		}
+	}
+	return nil
+}
+
+func (s *PostgresStore) Snapshot() Snapshot {
+	ctx := context.Background()
+	var snap Snapshot
+
+	matRows, _ := s.pool.Query(ctx, `SELECT id, title, source_type, body, created_at FROM ontology_materials`)
+	defer matRows.Close()
+	for matRows.Next() {
+		var m Material
+		matRows.Scan(&m.ID, &m.Title, &m.SourceType, &m.Body, &m.CreatedAt)
+		snap.Materials = append(snap.Materials, m)
+	}
+
+	cRows, _ := s.pool.Query(ctx, `SELECT id, concept_id, concept_label, summary, review_state, evidence, created_at FROM ontology_concepts`)
+	defer cRows.Close()
+	for cRows.Next() {
+		var c ConceptCandidate
+		var evidenceJSON string
+		cRows.Scan(&c.ID, &c.Concept.ID, &c.Concept.Label, &c.Summary, &c.ReviewState, &evidenceJSON, &c.CreatedAt)
+		json.Unmarshal([]byte(evidenceJSON), &c.Evidence)
+		snap.Concepts = append(snap.Concepts, c)
+	}
+
+	eRows, _ := s.pool.Query(ctx, `SELECT id, from_concept_id, to_concept_id, kind, evidence, created_at FROM ontology_edges`)
+	defer eRows.Close()
+	for eRows.Next() {
+		var e EdgeCandidate
+		var evidenceJSON string
+		eRows.Scan(&e.ID, &e.From.ID, &e.To.ID, &e.Kind, &evidenceJSON, &e.CreatedAt)
+		json.Unmarshal([]byte(evidenceJSON), &e.Evidence)
+		snap.Edges = append(snap.Edges, e)
+	}
+
+	gRows, _ := s.pool.Query(ctx, `SELECT id, concept_id, reason, evidence, created_at FROM ontology_gaps`)
+	defer gRows.Close()
+	for gRows.Next() {
+		var g Gap
+		var evidenceJSON string
+		gRows.Scan(&g.ID, &g.Concept.ID, &g.Reason, &evidenceJSON, &g.CreatedAt)
+		json.Unmarshal([]byte(evidenceJSON), &g.SupportingEvidence)
+		snap.Gaps = append(snap.Gaps, g)
+	}
+
+	return snap
+}