File size: 6,785 Bytes
ff453a6 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 | """SQLite persistence for projects, records, jobs, logs, and artifacts."""
from __future__ import annotations
import json
import sqlite3
from datetime import datetime, timezone
from pathlib import Path
from threading import Lock
from typing import Any
from uuid import uuid4
DB_PATH = Path(__file__).resolve().parent.parent / "data" / "platform.db"
_LOCK = Lock()
def utcnow() -> str:
return datetime.now(timezone.utc).isoformat()
def init_db(path: Path | None = None) -> None:
path = path or DB_PATH
path.parent.mkdir(parents=True, exist_ok=True)
with sqlite3.connect(path) as db:
db.executescript(
"""
CREATE TABLE IF NOT EXISTS projects (
project_id TEXT PRIMARY KEY, name TEXT NOT NULL, cancer_type TEXT NOT NULL,
metadata TEXT NOT NULL, created_at TEXT NOT NULL
);
CREATE TABLE IF NOT EXISTS records (
record_id TEXT PRIMARY KEY, project_id TEXT NOT NULL, kind TEXT NOT NULL,
payload TEXT NOT NULL, created_at TEXT NOT NULL,
FOREIGN KEY(project_id) REFERENCES projects(project_id)
);
CREATE INDEX IF NOT EXISTS idx_records_project_kind
ON records(project_id, kind);
CREATE TABLE IF NOT EXISTS jobs (
job_id TEXT PRIMARY KEY, project_id TEXT NOT NULL, operation TEXT NOT NULL,
status TEXT NOT NULL, input TEXT NOT NULL, output TEXT,
error TEXT, logs TEXT NOT NULL, created_at TEXT NOT NULL, updated_at TEXT NOT NULL
);
CREATE TABLE IF NOT EXISTS artifacts (
artifact_id TEXT PRIMARY KEY, project_id TEXT NOT NULL, job_id TEXT,
kind TEXT NOT NULL, name TEXT NOT NULL, media_type TEXT NOT NULL,
payload TEXT NOT NULL, created_at TEXT NOT NULL
);
"""
)
def _execute(sql: str, args: tuple = (), *, fetchone=False, fetchall=False):
with _LOCK, sqlite3.connect(DB_PATH) as db:
db.row_factory = sqlite3.Row
cur = db.execute(sql, args)
db.commit()
if fetchone:
row = cur.fetchone()
return dict(row) if row else None
if fetchall:
return [dict(row) for row in cur.fetchall()]
return cur.lastrowid
def create_project(name: str, cancer_type: str, metadata: dict) -> dict:
project_id = f"PRJ-{uuid4().hex[:12]}"
now = utcnow()
_execute(
"INSERT INTO projects VALUES (?,?,?,?,?)",
(project_id, name, cancer_type, json.dumps(metadata), now),
)
return get_project(project_id)
def get_project(project_id: str) -> dict | None:
row = _execute("SELECT * FROM projects WHERE project_id=?", (project_id,), fetchone=True)
if row:
row["metadata"] = json.loads(row["metadata"])
return row
def add_records(project_id: str, kind: str, payloads: list[dict]) -> list[str]:
ids = []
id_fields = {
"variant": "variant_id", "structure": "structure_id", "pocket": "pocket_id",
"compound": "compound_id", "docking": "docking_id", "md": "md_id",
"ranking": "ranking_id",
}
with _LOCK, sqlite3.connect(DB_PATH) as db:
for payload in payloads:
rid = payload.get(id_fields.get(kind, "record_id"))
rid = rid or f"{kind.upper()}-{uuid4().hex[:12]}"
db.execute(
"INSERT OR REPLACE INTO records VALUES (?,?,?,?,?)",
(rid, project_id, kind, json.dumps(payload, allow_nan=False), utcnow()),
)
ids.append(rid)
db.commit()
return ids
def get_record(project_id: str, kind: str, record_id: str) -> dict | None:
row = _execute(
"SELECT payload FROM records WHERE project_id=? AND kind=? AND record_id=?",
(project_id, kind, record_id),
fetchone=True,
)
return json.loads(row["payload"]) if row else None
def list_records(project_id: str, kind: str) -> list[dict]:
rows = _execute(
"SELECT payload FROM records WHERE project_id=? AND kind=? ORDER BY created_at",
(project_id, kind),
fetchall=True,
)
return [json.loads(row["payload"]) for row in rows]
def create_job(project_id: str, operation: str, input_data: dict) -> dict:
job_id = f"JOB-{uuid4().hex[:12]}"
now = utcnow()
_execute(
"INSERT INTO jobs VALUES (?,?,?,?,?,?,?,?,?,?)",
(job_id, project_id, operation, "queued", json.dumps(input_data), None, None, "[]", now, now),
)
return get_job(job_id)
def update_job(job_id: str, status: str, *, output: Any = None, error: str | None = None, log: str | None = None):
job = get_job(job_id)
logs = job["logs"] if job else []
if log:
logs.append({"at": utcnow(), "message": log})
_execute(
"UPDATE jobs SET status=?, output=?, error=?, logs=?, updated_at=? WHERE job_id=?",
(
status,
json.dumps(output, allow_nan=False) if output is not None else None,
error,
json.dumps(logs),
utcnow(),
job_id,
),
)
def get_job(job_id: str) -> dict | None:
row = _execute("SELECT * FROM jobs WHERE job_id=?", (job_id,), fetchone=True)
if not row:
return None
row["input"] = json.loads(row["input"])
row["output"] = json.loads(row["output"]) if row["output"] else None
row["logs"] = json.loads(row["logs"])
return row
def list_jobs(project_id: str) -> list[dict]:
rows = _execute(
"SELECT * FROM jobs WHERE project_id=? ORDER BY created_at DESC",
(project_id,),
fetchall=True,
)
for row in rows:
row["input"] = json.loads(row["input"])
row["output"] = json.loads(row["output"]) if row["output"] else None
row["logs"] = json.loads(row["logs"])
return rows
def add_artifact(project_id: str, kind: str, name: str, payload: Any, media_type: str, job_id: str | None = None) -> dict:
artifact_id = f"ART-{uuid4().hex[:12]}"
_execute(
"INSERT INTO artifacts VALUES (?,?,?,?,?,?,?,?)",
(artifact_id, project_id, job_id, kind, name, media_type, json.dumps(payload, allow_nan=False), utcnow()),
)
return get_artifact(artifact_id)
def get_artifact(artifact_id: str) -> dict | None:
row = _execute("SELECT * FROM artifacts WHERE artifact_id=?", (artifact_id,), fetchone=True)
if row:
row["payload"] = json.loads(row["payload"])
return row
def list_artifacts(project_id: str) -> list[dict]:
rows = _execute(
"SELECT artifact_id,project_id,job_id,kind,name,media_type,created_at FROM artifacts WHERE project_id=?",
(project_id,),
fetchall=True,
)
return rows
|