升级 NUPACK 4.1 并支持混合材料设计
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Lihatoo
parent
5daa60a464
commit
c6189d857d
33 changed files with 5830 additions and 466 deletions
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@ -13,6 +13,9 @@ from urllib.parse import urlencode
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from urllib.request import Request, urlopen
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DEFAULT_TRASH_RETENTION_SECONDS = 2 * 86400
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def _json_blob(value):
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if value is None:
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return None
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@ -127,8 +130,26 @@ class AccountStore:
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access_count INTEGER NOT NULL DEFAULT 0
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);
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CREATE INDEX IF NOT EXISTS shares_user_created_idx ON shares(user_id, created_at DESC);
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CREATE TABLE IF NOT EXISTS app_settings (
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key TEXT PRIMARY KEY,
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value TEXT NOT NULL,
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updated_at REAL NOT NULL
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);
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"""
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)
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job_columns = {
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row["name"] for row in connection.execute("PRAGMA table_info(jobs)").fetchall()
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}
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if "deleted_at" not in job_columns:
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connection.execute("ALTER TABLE jobs ADD COLUMN deleted_at REAL")
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if "purge_after" not in job_columns:
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connection.execute("ALTER TABLE jobs ADD COLUMN purge_after REAL")
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connection.execute(
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"CREATE INDEX IF NOT EXISTS jobs_deleted_idx ON jobs(deleted_at, purge_after)"
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)
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connection.execute(
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"DELETE FROM shares WHERE job_id IN (SELECT job_id FROM jobs WHERE deleted_at IS NOT NULL)"
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)
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self._initialized = True
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def upsert_user(self, user):
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@ -206,11 +227,15 @@ class AccountStore:
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row = connection.execute("SELECT user_id FROM jobs WHERE job_id = ?", (job_id,)).fetchone()
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return row["user_id"] if row else None
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def get_job(self, user_id, job_id, include_content=True):
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def get_job(self, user_id, job_id, include_content=True, include_deleted=False):
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self.initialize()
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columns = "*" if include_content else "job_id,user_id,status,source,created_at,updated_at,elapsed_seconds,workflow,mode,material,celsius,sodium,magnesium,max_size,strand_count,complex_count,compute_json,trials,stop_condition,max_time_seconds,stored_bytes"
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columns = "*" if include_content else "job_id,user_id,status,source,created_at,updated_at,elapsed_seconds,workflow,mode,material,celsius,sodium,magnesium,max_size,strand_count,complex_count,compute_json,trials,stop_condition,max_time_seconds,stored_bytes,deleted_at,purge_after"
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deleted_clause = "" if include_deleted else " AND deleted_at IS NULL"
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with self._connect() as connection:
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row = connection.execute(f"SELECT {columns} FROM jobs WHERE job_id = ? AND user_id = ?", (job_id, user_id)).fetchone()
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row = connection.execute(
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f"SELECT {columns} FROM jobs WHERE job_id = ? AND user_id = ?{deleted_clause}",
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(job_id, user_id),
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).fetchone()
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return self._job_row(row, include_content=include_content) if row else None
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def list_jobs(self, user_id, filters=None):
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@ -218,7 +243,8 @@ class AccountStore:
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filters = filters or {}
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limit = min(100, max(1, int(filters.get("limit", 30))))
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offset = max(0, int(filters.get("offset", 0)))
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clauses = ["user_id = ?"]
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self.purge_expired_jobs()
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clauses = ["user_id = ?", "deleted_at IS NULL"]
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values = [user_id]
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for field in ("status", "workflow", "mode", "material"):
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value = str(filters.get(field) or "").strip()
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@ -230,7 +256,7 @@ class AccountStore:
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clauses.append("(job_id LIKE ? OR workflow LIKE ? OR mode LIKE ? OR material LIKE ?)")
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values.extend([f"%{search}%"] * 4)
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where = " AND ".join(clauses)
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columns = "job_id,user_id,status,source,created_at,updated_at,elapsed_seconds,workflow,mode,material,celsius,sodium,magnesium,max_size,strand_count,complex_count,compute_json,trials,stop_condition,max_time_seconds,stored_bytes"
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columns = "job_id,user_id,status,source,created_at,updated_at,elapsed_seconds,workflow,mode,material,celsius,sodium,magnesium,max_size,strand_count,complex_count,compute_json,trials,stop_condition,max_time_seconds,stored_bytes,deleted_at,purge_after"
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with self._connect() as connection:
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total = connection.execute(f"SELECT count(*) AS count FROM jobs WHERE {where}", values).fetchone()["count"]
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rows = connection.execute(
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@ -239,6 +265,51 @@ class AccountStore:
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).fetchall()
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return {"items": [self._job_row(row, include_content=False) for row in rows], "total": total, "limit": limit, "offset": offset}
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def list_all_jobs(self, filters=None):
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self.initialize()
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filters = filters or {}
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limit = min(200, max(1, int(filters.get("limit", 50))))
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offset = max(0, int(filters.get("offset", 0)))
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self.purge_expired_jobs()
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deleted = str(filters.get("deleted") or "0").strip() == "1"
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clauses = ["j.deleted_at IS NOT NULL" if deleted else "j.deleted_at IS NULL"]
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values = []
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for field in ("status", "workflow", "mode", "material"):
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value = str(filters.get(field) or "").strip()
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if value:
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clauses.append(f"j.{field} = ?")
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values.append(value)
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search = str(filters.get("q") or "").strip()
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if search:
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clauses.append(
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"(j.job_id LIKE ? OR j.user_id LIKE ? OR u.username LIKE ? OR "
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"coalesce(u.email, '') LIKE ? OR j.workflow LIKE ? OR j.mode LIKE ?)"
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)
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values.extend([f"%{search}%"] * 6)
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where = f"WHERE {' AND '.join(clauses)}" if clauses else ""
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columns = (
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"j.job_id,j.user_id,j.status,j.source,j.created_at,j.updated_at,j.elapsed_seconds,"
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"j.workflow,j.mode,j.material,j.celsius,j.sodium,j.magnesium,j.max_size,"
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"j.strand_count,j.complex_count,j.compute_json,j.trials,j.stop_condition,"
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"j.max_time_seconds,j.stored_bytes,j.deleted_at,j.purge_after,u.username,u.email,u.display_name"
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)
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with self._connect() as connection:
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total = connection.execute(
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f"SELECT count(*) AS count FROM jobs j JOIN users u ON u.user_id=j.user_id {where}",
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values,
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).fetchone()["count"]
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rows = connection.execute(
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f"SELECT {columns} FROM jobs j JOIN users u ON u.user_id=j.user_id "
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f"{where} ORDER BY j.created_at DESC LIMIT ? OFFSET ?",
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[*values, limit, offset],
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).fetchall()
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return {
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"items": [self._job_row(row, include_content=False) for row in rows],
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"total": total,
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"limit": limit,
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"offset": offset,
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}
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def usage(self, user_id):
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self.initialize()
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with self._connect() as connection:
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@ -248,7 +319,7 @@ class AccountStore:
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coalesce(sum(CASE WHEN status='error' THEN 1 ELSE 0 END),0) AS error_jobs,
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coalesce(sum(CASE WHEN status IN ('queued','running','cancel_requested') THEN 1 ELSE 0 END),0) AS active_jobs,
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coalesce(sum(elapsed_seconds),0) AS compute_seconds,
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coalesce(sum(stored_bytes),0) AS stored_bytes FROM jobs WHERE user_id=?""",
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coalesce(sum(stored_bytes),0) AS stored_bytes FROM jobs WHERE user_id=? AND deleted_at IS NULL""",
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(user_id,),
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).fetchone()
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shares = connection.execute("SELECT count(*) AS count FROM shares WHERE user_id=? AND active=1", (user_id,)).fetchone()["count"]
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@ -279,17 +350,86 @@ class AccountStore:
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imported += 1
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return imported
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def delete_job(self, user_id, job_id):
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def trash_retention_seconds(self):
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self.initialize()
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with self._connect() as connection:
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row = connection.execute("SELECT status FROM jobs WHERE job_id=? AND user_id=?", (job_id, user_id)).fetchone()
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row = connection.execute(
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"SELECT value FROM app_settings WHERE key='trash_retention_seconds'"
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).fetchone()
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try:
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return max(3600, int(row["value"])) if row else DEFAULT_TRASH_RETENTION_SECONDS
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except (TypeError, ValueError):
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return DEFAULT_TRASH_RETENTION_SECONDS
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def set_trash_retention_days(self, days):
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days = float(days)
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if not 1 / 24 <= days <= 365:
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raise ValueError("Trash retention must be between 1 hour and 365 days.")
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seconds = int(days * 86400)
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self.initialize()
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with self._connect() as connection:
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connection.execute(
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"""INSERT INTO app_settings(key,value,updated_at) VALUES('trash_retention_seconds',?,?)
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ON CONFLICT(key) DO UPDATE SET value=excluded.value,updated_at=excluded.updated_at""",
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(str(seconds), time.time()),
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)
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return seconds
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def purge_expired_jobs(self):
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self.initialize()
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with self._connect() as connection:
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cursor = connection.execute(
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"DELETE FROM jobs WHERE deleted_at IS NOT NULL AND purge_after IS NOT NULL AND purge_after <= ?",
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(time.time(),),
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)
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return cursor.rowcount
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def delete_job(self, user_id, job_id):
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self.initialize()
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now = time.time()
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retention_seconds = self.trash_retention_seconds()
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with self._connect() as connection:
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row = connection.execute(
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"SELECT status,deleted_at FROM jobs WHERE job_id=? AND user_id=?",
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(job_id, user_id),
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).fetchone()
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if row is None:
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return False
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if row["status"] in {"queued", "running", "cancel_requested"}:
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raise ValueError("Active jobs cannot be deleted.")
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connection.execute("DELETE FROM jobs WHERE job_id=? AND user_id=?", (job_id, user_id))
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if row["deleted_at"] is not None:
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return False
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connection.execute(
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"UPDATE jobs SET deleted_at=?,purge_after=?,updated_at=? WHERE job_id=? AND user_id=?",
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(now, now + retention_seconds, now, job_id, user_id),
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)
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connection.execute("DELETE FROM shares WHERE job_id=?", (job_id,))
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return True
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def admin_trash_job(self, job_id):
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self.initialize()
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with self._connect() as connection:
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row = connection.execute("SELECT user_id FROM jobs WHERE job_id=?", (job_id,)).fetchone()
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return self.delete_job(row["user_id"], job_id) if row else False
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def restore_job(self, job_id):
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self.initialize()
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with self._connect() as connection:
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cursor = connection.execute(
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"UPDATE jobs SET deleted_at=NULL,purge_after=NULL,updated_at=? WHERE job_id=? AND deleted_at IS NOT NULL",
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(time.time(), job_id),
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)
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return cursor.rowcount > 0
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def permanently_delete_job(self, job_id):
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self.initialize()
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with self._connect() as connection:
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cursor = connection.execute(
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"DELETE FROM jobs WHERE job_id=? AND deleted_at IS NOT NULL",
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(job_id,),
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)
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return cursor.rowcount > 0
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def create_share(self, user_id, job_id, expires_in=None):
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job = self.get_job(user_id, job_id, include_content=False)
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if job is None:
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@ -298,6 +438,19 @@ class AccountStore:
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expires_at = now + int(expires_in) if expires_in else None
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share_id = uuid_token(18)
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with self._connect() as connection:
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existing = connection.execute(
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"""SELECT * FROM shares
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WHERE user_id=? AND job_id=? AND active=1
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AND (expires_at IS NULL OR expires_at>?)
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ORDER BY created_at DESC LIMIT 1""",
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(user_id, job_id, now),
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).fetchone()
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if existing is not None:
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return dict(existing)
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connection.execute(
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"DELETE FROM shares WHERE user_id=? AND job_id=?",
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(user_id, job_id),
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)
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connection.execute(
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"INSERT INTO shares(share_id,job_id,user_id,active,created_at,expires_at) VALUES(?,?,?,?,?,?)",
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(share_id, job_id, user_id, 1, now, expires_at),
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@ -329,7 +482,8 @@ class AccountStore:
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with self._connect() as connection:
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rows = connection.execute(
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"""SELECT s.*,j.status,j.workflow,j.mode,j.material,j.created_at AS job_created_at
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FROM shares s JOIN jobs j ON j.job_id=s.job_id WHERE s.user_id=? ORDER BY s.created_at DESC""",
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FROM shares s JOIN jobs j ON j.job_id=s.job_id
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WHERE s.user_id=? AND j.deleted_at IS NULL ORDER BY s.created_at DESC""",
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(user_id,),
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).fetchall()
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return [dict(row) for row in rows]
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@ -344,6 +498,14 @@ class AccountStore:
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share = self.get_share_for_owner(user_id, share_id)
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if share is None:
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return None
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if active is False:
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with self._connect() as connection:
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connection.execute(
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"DELETE FROM shares WHERE share_id=? AND user_id=?",
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(share_id, user_id),
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)
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share["active"] = 0
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return share
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fields = []
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values = []
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if active is not None:
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