Patterns for SQLite databases in Python projects - state management, caching, and async operations. Triggers on: sqlite, sqlite3, aiosqlite, local database, database schema, migration, wal mode.
npx skills add https://github.com/aiskillstore/marketplace --skill sqlite-ops
Patterns for SQLite databases in Python projects.
import sqlite3
def get_connection(db_path: str) -> sqlite3.Connection:
conn = sqlite3.connect(db_path, check_same_thread=False)
conn.row_factory = sqlite3.Row # Dict-like access
conn.execute("PRAGMA journal_mode=WAL") # Better concurrency
conn.execute("PRAGMA foreign_keys=ON")
return conn
from contextlib import contextmanager
@contextmanager
def db_transaction(conn: sqlite3.Connection):
try:
yield conn
conn.commit()
except Exception:
conn.rollback()
raise
Enable for concurrent read/write:
conn.execute("PRAGMA journal_mode=WAL")
| Mode | Reads | Writes | Best For |
|------|-------|--------|----------|
| DELETE (default) | Blocked during write | Single | Simple scripts |
| WAL | Concurrent | Single | Web apps, MCP servers |
| Issue | Solution |
|-------|----------|
| "database is locked" | Use WAL mode |
| Slow queries | Add indexes, check EXPLAIN QUERY PLAN |
| Thread safety | Use check_same_thread=False |
| FK not enforced | Run PRAGMA foreign_keys=ON |
sqlite3 mydb.sqlite # Open database
.tables # Show tables
.schema items # Show schema
.headers on && .mode csv && .output data.csv # Export CSV
VACUUM; # Reclaim space
For detailed patterns, load:
./references/schema-patterns.md - State, cache, event, queue table designs./references/async-patterns.md - aiosqlite CRUD, batching, connection pools./references/migration-patterns.md - Version migrations, JSON handlingEfficient 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 aiskillstore/sqlite-ops 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.