Provides patterns to implement persistence layers with Spring Data JPA. Use when creating repositories, configuring entity relationships, writing queries (derived and `@Query`), setting up pagination, database auditing, transactions, UUID primary keys, multiple databases, and database indexing.
npx skills add https://github.com/giuseppe-trisciuoglio/developer-kit --skill spring-data-jpa
Provides patterns for Spring Data JPA repositories, entity relationships, queries, pagination, auditing, and transactions.
Creating repositories with CRUD operations, entity relationships, @Query annotations, pagination, auditing, or UUID primary keys.
To implement a repository interface:
@Repository
public interface UserRepository extends JpaRepository<User, Long> {
// Custom methods defined here
}
Optional<User> findByEmail(String email);
List<User> findByStatusOrderByCreatedDateDesc(String status);
@Query: @Query("SELECT u FROM User u WHERE u.status = :status")
List<User> findActiveUsers(@Param("status") String status);
@Entity
@Table(name = "users")
public class User {
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id;
@Column(nullable = false, length = 100)
private String email;
}
@OneToMany(mappedBy = "user", cascade = CascadeType.ALL, orphanRemoval = true)
private List<Order> orders = new ArrayList<>();
Validation: Test cascade behavior with a small dataset before applying to production data. Verify delete operations don't cascade unexpectedly.
@CreatedDate
@Column(nullable = false, updatable = false)
private LocalDateTime createdDate;
@Query for complex queries@Modifying for update/delete operations@Transactional(readOnly = true)1. Verify entity configuration:
2. Optimize query performance:
EXPLAIN ANALYZE on queries against large tables@EntityGraph to prevent N+1 queries3. Validate pagination:
@Repository
public interface ProductRepository extends JpaRepository<Product, Long> {
// Derived query
List<Product> findByCategory(String category);
// Custom query
@Query("SELECT p FROM Product p WHERE p.price > :minPrice")
List<Product> findExpensiveProducts(@Param("minPrice") BigDecimal minPrice);
}
@Service
public class ProductService {
private final ProductRepository repository;
public Page<Product> getProducts(int page, int size) {
Pageable pageable = PageRequest.of(page, size, Sort.by("name").ascending());
return repository.findAll(pageable);
}
}
@Entity
@EntityListeners(AuditingEntityListener.class)
public class Order {
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id;
@CreatedDate
@Column(nullable = false, updatable = false)
private LocalDateTime createdDate;
@LastModifiedDate
private LocalDateTime lastModifiedDate;
@CreatedBy
@Column(nullable = false, updatable = false)
private String createdBy;
}
final modifiers@Value for DTOs@Id and @GeneratedValue annotations@Table and @Column annotations@EntityGraph to avoid N+1 query problemsFor comprehensive examples, detailed patterns, and advanced configurations, see:
@EntityGraph or JOIN FETCH in queries.CascadeType.REMOVE on large collections as it can cause performance issues.EAGER fetch type for collections; it can cause excessive database queries.@Transactional(readOnly = true) for read operations to enable optimizations.Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
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