> Use when creating database migrations, schema changes, seed data, or any SQL that modifies database structure. Covers Flyway naming conventions, versioning, and safe migration patterns.
npx skills add https://github.com/rrezartprebreza/spring-boot-skills --skill flyway-migrations
Boot's modular starters do NOT pull Flyway in transitively — spring-boot-starter-data-jpa
alone means migrations silently never run. Add the Flyway starter plus your database's module:
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-flyway</artifactId>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-database-postgresql</artifactId> <!-- DB-specific module is required -->
</dependency>
src/main/resources/db/migration/
V{version}__{description}.sql ← versioned (run once)
R__{description}.sql ← repeatable (run when checksum changes)
U{version}__{description}.sql ← undo (requires Flyway Teams)
Examples:
V1__create_users_table.sql
V2__create_orders_table.sql
V2.1__add_order_status_index.sql
V3__add_customer_email_to_orders.sql
R__create_reporting_views.sql
Rules:
__ between version and description_ for spaces in description-- V1__create_users_table.sql
CREATE TABLE users (
id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
email VARCHAR(255) NOT NULL UNIQUE,
password VARCHAR(255) NOT NULL,
role VARCHAR(50) NOT NULL DEFAULT 'USER',
created_at TIMESTAMPTZ NOT NULL DEFAULT NOW(),
updated_at TIMESTAMPTZ NOT NULL DEFAULT NOW()
);
CREATE INDEX idx_users_email ON users(email);
-- V2__create_orders_table.sql
CREATE TABLE orders (
id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
user_id UUID NOT NULL REFERENCES users(id),
status VARCHAR(50) NOT NULL DEFAULT 'PENDING',
total_amount NUMERIC(12, 2) NOT NULL DEFAULT 0,
created_at TIMESTAMPTZ NOT NULL DEFAULT NOW(),
updated_at TIMESTAMPTZ NOT NULL DEFAULT NOW()
);
CREATE INDEX idx_orders_user_id ON orders(user_id);
CREATE INDEX idx_orders_status ON orders(status);
CREATE INDEX idx_orders_created ON orders(created_at DESC);
-- V3__add_shipping_address_to_orders.sql
-- Adding a column — always nullable or with default (safe for existing rows)
ALTER TABLE orders
ADD COLUMN shipping_address TEXT,
ADD COLUMN shipped_at TIMESTAMPTZ;
-- ✅ Safe: add nullable column
ALTER TABLE orders ADD COLUMN notes TEXT;
-- ✅ Safe: add column with default
ALTER TABLE orders ADD COLUMN priority INT NOT NULL DEFAULT 0;
-- ✅ Safe: add index CONCURRENTLY (no table lock in Postgres)
-- ⚠️ BUT: CONCURRENTLY cannot run inside a transaction, and Flyway wraps every
-- migration in one by default → the migration FAILS. Opt that one script out
-- with a sidecar config file:
-- V4__add_orders_email_index.sql.conf → executeInTransaction=false
-- Keep the CONCURRENTLY statement alone in its own migration file.
CREATE INDEX CONCURRENTLY idx_orders_email ON orders(customer_email);
-- ✅ Safe: rename via add + backfill + drop (multi-step)
-- Step 1 (V5): add new column
ALTER TABLE orders ADD COLUMN customer_email VARCHAR(255);
-- Step 2 (V5): backfill
UPDATE orders SET customer_email = (SELECT email FROM users WHERE users.id = orders.user_id);
-- Step 3 (V5): add constraint after data is there
ALTER TABLE orders ALTER COLUMN customer_email SET NOT NULL;
-- Step 4 (later V6, after code is deployed): drop old column
ALTER TABLE orders DROP COLUMN user_id;
-- ❌ Dangerous: rename column directly (breaks running app)
ALTER TABLE orders RENAME COLUMN user_id TO customer_id;
-- ❌ Dangerous: NOT NULL without default on large table (locks table)
ALTER TABLE orders ADD COLUMN priority INT NOT NULL; -- will fail on existing rows
spring:
flyway:
enabled: true
locations: classpath:db/migration
baseline-on-migrate: true # for existing databases
validate-on-migrate: true
out-of-order: false # enforce sequential execution
// Use Spring profiles, not Flyway, for seed data
@Component
@Profile("dev")
@RequiredArgsConstructor
public class DevDataSeeder implements ApplicationRunner {
private final UserRepository userRepository;
@Override
public void run(ApplicationArguments args) {
if (userRepository.count() == 0) {
userRepository.save(User.createAdmin("[email protected]", "password123"));
}
}
}
V20260414_1__)flyway info before committing to check for version gaps or duplicatesflyway validate as a pre-deploy step to catch conflicts earlyout-of-order: true in production — it masks migration ordering bugsV1_create_users.sql (single underscore) — must be double __NOT NULL column without default — use nullable or provide default@Profile("dev") seeders insteadCREATE INDEX CONCURRENTLY in a normal migration — fails inside Flyway's transaction; needs executeInTransaction=false in a .sql.conf sidecar and its own fileDROP TABLE or DROP COLUMN as first step — always add new column, deploy code, then drop old in a later migrationflyway-core — database support lives in flyway-database-<db> modules; without it startup fails with "Unsupported Database"spring-boot-starter-flyway yourselfEfficient 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.
Take rrezartprebreza/spring-boot-flyway-migrations from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.