Mod: database is now stable.
Improved convenience and documention.
This commit is contained in:
parent
00f7279c6d
commit
a4e9a8f8dc
2
.vscode/settings.json
vendored
2
.vscode/settings.json
vendored
@ -8,5 +8,5 @@
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": false,
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"python.linting.flake8Enabled": true,
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"python.linting.flake8Args": ["--ignore=E402,E251,E501,E201,E202,W293,W291,W504", "--verbose"]
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"python.linting.flake8Args": ["--ignore=E402,E251,E501,E201,E202,W293,W291,W504,E203", "--verbose"]
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}
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@ -1,11 +1,13 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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from .models import __models__
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from .db import Database
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from . import utils
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from . import tables
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class tables:
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pass
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from .database import Database
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for model in __models__:
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setattr(tables, model.__name__, model)
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__all__ = [
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"utils",
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"tables",
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"Database"
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]
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238
anisotropy/database/database.py
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238
anisotropy/database/database.py
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@ -0,0 +1,238 @@
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# -*- coding: utf-8 -*-
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from __future__ import annotations
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from numpy import ndarray
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import peewee as pw
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import pathlib
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import time
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from . import tables
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class Database(pw.SqliteDatabase):
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def __init__(self, *args, **kwargs):
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"""A Database object contains SQLite database with convient
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properties and methods
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"""
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self.filepath = kwargs.get("path", None)
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self.pragmas_ = kwargs.get("pragmas", { "foreign_keys": 1, "journal_mode": "wal" })
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self.field_types_ = kwargs.get("field_types", { "list": "text" })
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self.autoconnect_ = kwargs.get("autoconnect", False)
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pw.SqliteDatabase.__init__(
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self,
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None,
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pragmas = self.pragmas_,
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field_types = self.field_types_,
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autoconnect = self.autoconnect_
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)
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if self.filepath:
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self.setup()
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@property
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def tables(self) -> list:
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"""Return all tables as list.
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"""
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return [ tables.__dict__[table] for table in tables.__all__ ]
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def setup(self, filename: str = None):
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"""Initialize database and create tables.
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:param filename:
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Path to the file.
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:return:
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Self.
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"""
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self.filepath = pathlib.Path(filename or self.filepath).resolve()
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self.init(
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self.filepath,
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pragmas = self.pragmas_
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)
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tables.database_proxy.initialize(self)
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with self:
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self.create_tables(self.tables)
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return self
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def csave(self, table: pw.Model, tries: int = 100):
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"""Try to save data from model to the database ignoring
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peewee.OperationalError. Usefull for concurrent processes.
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:param table:
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Table to save.
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:param tries:
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Number of tries. Falling to sleep for 1 second if database
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is locked.
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"""
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while tries >= 0:
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if self.is_closed():
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self.connect()
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try:
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table.save()
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except pw.OperationalError:
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tries -= 1
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time.sleep(1)
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else:
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self.close()
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break
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def getExecution(self, idn: int) -> tables.Execution | None:
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"""Get execution entry from database.
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:param idn:
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Index of the execution.
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:return:
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If entry is found returns Model instance else None.
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"""
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query = tables.Execution.select().where(tables.Execution.exec_id == idn)
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with self:
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table = query.get() if query.exists() else None
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return table
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def getLatest(self) -> tables.Execution | None:
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"""Get latest execution entry from database.
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:return:
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If entry is found returns Model instance else None.
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"""
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query = tables.Execution.select()
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with self:
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table = query[-1] if query.exists() else None
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return table
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def getShape(
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self,
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label: str = None,
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direction: list[float] | ndarray = None,
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alpha: float = None,
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execution: int = None,
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**kwargs
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) -> tables.Shape | None:
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"""Get shape entry from database.
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:param label:
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Label of the shape.
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:param direction:
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Array of floats represents direction vector.
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:param alpha:
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Spheres overlap parameter.
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:param execution:
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Index of the execution. If None, use latest.
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:return:
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If entry is found returns Model instance else None.
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"""
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execution = execution or self.getLatest()
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query = (
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tables.Shape
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.select()
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.join(tables.Execution, pw.JOIN.LEFT_OUTER)
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.where(
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tables.Execution.exec_id == execution,
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tables.Shape.label == label,
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tables.Shape.direction == direction,
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tables.Shape.alpha == alpha
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)
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)
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with self:
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table = query.get() if query.exists() else None
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return table
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def getMesh(
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self,
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label: str = None,
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direction: list[float] | ndarray = None,
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alpha: float = None,
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execution: int = None,
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**kwargs
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) -> tables.Mesh | None:
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"""Get mesh entry from database.
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:param label:
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Label of the shape.
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:param direction:
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Array of floats represents direction vector.
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:param alpha:
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Spheres overlap parameter.
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:param execution:
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Index of the execution. If None, use latest.
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:return:
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If entry is found returns Model instance else None.
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"""
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execution = execution or self.getLatest()
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query = (
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tables.Mesh
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.select()
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.join(tables.Shape, pw.JOIN.LEFT_OUTER)
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.join(tables.Execution, pw.JOIN.LEFT_OUTER)
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.where(
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tables.Execution.exec_id == execution,
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tables.Shape.label == label,
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tables.Shape.direction == direction,
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tables.Shape.alpha == alpha
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)
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)
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with self:
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table = query.get() if query.exists() else None
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return table
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def getFlowOnephase(
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self,
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label: str = None,
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direction: list[float] | ndarray = None,
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alpha: float = None,
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execution: int = None,
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to_dict: bool = False,
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**kwargs
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) -> tables.Mesh | dict | None:
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"""Get one phase flow entry from database.
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:param label:
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Label of the shape.
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:param direction:
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Array of floats represents direction vector.
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:param alpha:
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Spheres overlap parameter.
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:param execution:
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Index of the execution. If None, use latest.
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:param to_dict:
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If True, convert result to dict.
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:return:
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If entry is found returns Model instance or dict else None.
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"""
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execution = execution or self.getLatest()
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query = (
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tables.FlowOnephase
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.select()
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.join(tables.Mesh, pw.JOIN.LEFT_OUTER)
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.join(tables.Shape, pw.JOIN.LEFT_OUTER)
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.join(tables.Execution, pw.JOIN.LEFT_OUTER)
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.where(
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tables.Execution.exec_id == execution,
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tables.Shape.label == label,
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tables.Shape.direction == direction,
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tables.Shape.alpha == alpha
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)
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)
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with self:
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if to_dict:
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table = query.dicts().get() if query.exists() else None
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else:
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table = query.get() if query.exists() else None
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return table
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@ -1,140 +0,0 @@
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# -*- coding: utf-8 -*-
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# This file is part of anisotropy.
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# License: GNU GPL version 3, see the file "LICENSE" for details.
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import os
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from peewee import SqliteDatabase, JOIN, OperationalError
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from . import models
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class Database(SqliteDatabase):
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def __init__(self, *args, **kwargs):
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self.filepath = kwargs.get("path", None)
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self.pragmas_ = kwargs.get("pragmas", { "foreign_keys": 1, "journal_mode": "wal" })
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self.field_types_ = kwargs.get("field_types", { "list": "text" })
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self.autoconnect_ = kwargs.get("autoconnect", False)
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SqliteDatabase.__init__(
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self,
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None,
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pragmas = self.pragmas_,
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field_types = self.field_types_,
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autoconnect = self.autoconnect_
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)
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if self.filepath:
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self.setup()
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@property
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def tables(self):
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return models.__models__
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def setup(self, filename: str = None):
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#if not self.filepath:
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self.filepath = os.path.abspath(filename or self.filepath)
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self.init(
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self.filepath,
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pragmas = self.pragmas_,
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#field_types = self.field_types_,
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#autoconnect = self.autoconnect_
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)
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models.__database_proxy__.initialize(self)
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with self:
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self.create_tables(self.tables)
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def csave(self, table, tries: int = 100):
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while tries >= 0:
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if self.is_closed():
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self.connect()
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try:
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table.save()
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except OperationalError as e:
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logger.debug(e)
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tries -= 1
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time.sleep(1)
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else:
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self.close()
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break
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def getExecution(self, idn):
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query = models.Execution.select().where(models.Execution.exec_id == idn)
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with self:
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table = query.get() if query.exists() else None
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return table
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def getLatest(self):
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query = models.Execution.select()
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with self:
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table = query[-1] if query.exists() else None
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return table
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def getShape(self, label = None, direction = None, alpha = None, execution = None, **kwargs):
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execution = execution or self.getLatest()
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query = (
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models.Shape
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.select()
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.join(models.Execution, JOIN.LEFT_OUTER)
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.where(
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models.Execution.exec_id == execution,
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models.Shape.label == label,
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models.Shape.direction == direction,
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models.Shape.alpha == alpha
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)
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)
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with self:
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table = query.get() if query.exists() else None
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return table
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def getMesh(self, label = None, direction = None, alpha = None, execution = None, **kwargs):
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execution = execution or self.getLatest()
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query = (
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models.Mesh
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.select()
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.join(models.Shape, JOIN.LEFT_OUTER)
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.join(models.Execution, JOIN.LEFT_OUTER)
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.where(
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models.Execution.exec_id == execution,
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models.Shape.label == label,
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models.Shape.direction == direction,
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models.Shape.alpha == alpha
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)
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)
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with self:
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table = query.get() if query.exists() else None
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return table
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def getFlowOnephase(self, label = None, direction = None, alpha = None, execution = None, to_dict = False, **kwargs):
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execution = execution or self.getLatest()
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query = (
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models.FlowOnephase
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.select()
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.join(models.Mesh, JOIN.LEFT_OUTER)
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.join(models.Shape, JOIN.LEFT_OUTER)
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.join(models.Execution, JOIN.LEFT_OUTER)
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.where(
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models.Execution.exec_id == execution,
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models.Shape.label == label,
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models.Shape.direction == direction,
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models.Shape.alpha == alpha
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)
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)
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with self:
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if to_dict:
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table = query.dicts().get() if query.exists() else None
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else:
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table = query.get() if query.exists() else None
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return table
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@ -1,108 +0,0 @@
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# -*- coding: utf-8 -*-
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# This file is part of anisotropy.
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# License: GNU GPL version 3, see the file "LICENSE" for details.
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from peewee import (
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SqliteDatabase, JOIN,
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Model, Field,
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AutoField, ForeignKeyField,
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TextField, FloatField,
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IntegerField, BooleanField,
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TimeField, DateTimeField, Proxy
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)
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from .utils import JSONField
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__database_proxy__ = Proxy()
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class Execution(Model):
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exec_id = AutoField()
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date = DateTimeField()
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executionTime = TimeField(null = True)
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class Meta:
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database = __database_proxy__
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table_name = "executions"
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class Shape(Model):
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shape_id = AutoField()
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exec_id = ForeignKeyField(Execution, backref = "executions", on_delete = "CASCADE")
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shapeStatus = TextField(null = True, default = "idle")
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shapeExecutionTime = TimeField(null = True)
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label = TextField(null = True)
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direction = JSONField(null = True)
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alpha = FloatField(null = True)
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r0 = FloatField(null = True)
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L = FloatField(null = True)
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radius = FloatField(null = True)
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filletsEnabled = BooleanField(null = True)
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fillets = FloatField(null = True)
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volumeCell = FloatField(null = True)
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volume = FloatField(null = True)
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porosity = FloatField(null = True)
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class Meta:
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database = __database_proxy__
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table_name = "shapes"
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#depends_on = Execution
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class Mesh(Model):
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mesh_id = AutoField()
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shape_id = ForeignKeyField(Shape, backref = "shapes", on_delete = "CASCADE")
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meshStatus = TextField(null = True, default = "idle")
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meshExecutionTime = TimeField(null = True)
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elements = IntegerField(null = True)
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edges = IntegerField(null = True)
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faces = IntegerField(null = True)
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volumes = IntegerField(null = True)
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tetrahedrons = IntegerField(null = True)
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prisms = IntegerField(null = True)
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pyramids = IntegerField(null = True)
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class Meta:
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database = __database_proxy__
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table_name = "meshes"
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#depends_on = Execution
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class FlowOnephase(Model):
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flow_id = AutoField()
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mesh_id = ForeignKeyField(Mesh, backref = "meshes", on_delete = "CASCADE")
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flowStatus = TextField(null = True, default = "idle")
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flowExecutionTime = TimeField(null = True)
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pressureInlet = FloatField(null = True)
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pressureOutlet = FloatField(null = True)
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pressureInternal = FloatField(null = True)
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velocityInlet = JSONField(null = True)
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velocityOutlet = JSONField(null = True)
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velocityInternal = JSONField(null = True)
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viscosity = FloatField(null = True)
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viscosityKinematic = FloatField(null = True)
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density = FloatField(null = True)
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flowRate = FloatField(null = True)
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permeability = FloatField(null = True)
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class Meta:
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database = __database_proxy__
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table_name = "flows"
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#depends_on = Execution
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__models__ = [
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Execution,
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Shape,
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Mesh,
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FlowOnephase
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]
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102
anisotropy/database/tables.py
Normal file
102
anisotropy/database/tables.py
Normal file
@ -0,0 +1,102 @@
|
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# -*- coding: utf-8 -*-
|
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|
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import peewee as pw
|
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|
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from . import utils
|
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|
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|
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# proxy, assign database later
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database_proxy = pw.Proxy()
|
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|
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class Execution(pw.Model):
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exec_id = pw.AutoField()
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date = pw.DateTimeField()
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executionTime = pw.TimeField(null = True)
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class Meta:
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database = database_proxy
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table_name = "executions"
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class Shape(pw.Model):
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shape_id = pw.AutoField()
|
||||
exec_id = pw.ForeignKeyField(Execution, backref = "executions", on_delete = "CASCADE")
|
||||
|
||||
shapeStatus = pw.TextField(null = True, default = "idle")
|
||||
shapeExecutionTime = pw.TimeField(null = True)
|
||||
|
||||
label = pw.TextField(null = True)
|
||||
direction = utils.JSONField(null = True)
|
||||
alpha = pw.FloatField(null = True)
|
||||
|
||||
r0 = pw.FloatField(null = True)
|
||||
L = pw.FloatField(null = True)
|
||||
radius = pw.FloatField(null = True)
|
||||
|
||||
filletsEnabled = pw.BooleanField(null = True)
|
||||
fillets = pw.FloatField(null = True)
|
||||
|
||||
volumeCell = pw.FloatField(null = True)
|
||||
volume = pw.FloatField(null = True)
|
||||
porosity = pw.FloatField(null = True)
|
||||
|
||||
class Meta:
|
||||
database = database_proxy
|
||||
table_name = "shapes"
|
||||
# depends_on = Execution
|
||||
|
||||
|
||||
class Mesh(pw.Model):
|
||||
mesh_id = pw.AutoField()
|
||||
shape_id = pw.ForeignKeyField(Shape, backref = "shapes", on_delete = "CASCADE")
|
||||
|
||||
meshStatus = pw.TextField(null = True, default = "idle")
|
||||
meshExecutionTime = pw.TimeField(null = True)
|
||||
|
||||
elements = pw.IntegerField(null = True)
|
||||
edges = pw.IntegerField(null = True)
|
||||
faces = pw.IntegerField(null = True)
|
||||
volumes = pw.IntegerField(null = True)
|
||||
tetrahedrons = pw.IntegerField(null = True)
|
||||
prisms = pw.IntegerField(null = True)
|
||||
pyramids = pw.IntegerField(null = True)
|
||||
|
||||
class Meta:
|
||||
database = database_proxy
|
||||
table_name = "meshes"
|
||||
# depends_on = Execution
|
||||
|
||||
|
||||
class FlowOnephase(pw.Model):
|
||||
flow_id = pw.AutoField()
|
||||
mesh_id = pw.ForeignKeyField(Mesh, backref = "meshes", on_delete = "CASCADE")
|
||||
|
||||
flowStatus = pw.TextField(null = True, default = "idle")
|
||||
flowExecutionTime = pw.TimeField(null = True)
|
||||
|
||||
pressureInlet = pw.FloatField(null = True)
|
||||
pressureOutlet = pw.FloatField(null = True)
|
||||
pressureInternal = pw.FloatField(null = True)
|
||||
velocityInlet = utils.JSONField(null = True)
|
||||
velocityOutlet = utils.JSONField(null = True)
|
||||
velocityInternal = utils.JSONField(null = True)
|
||||
viscosity = pw.FloatField(null = True)
|
||||
viscosityKinematic = pw.FloatField(null = True)
|
||||
density = pw.FloatField(null = True)
|
||||
flowRate = pw.FloatField(null = True)
|
||||
permeability = pw.FloatField(null = True)
|
||||
|
||||
class Meta:
|
||||
database = database_proxy
|
||||
table_name = "flows"
|
||||
# depends_on = Execution
|
||||
|
||||
|
||||
__all__ = [
|
||||
"Execution",
|
||||
"Shape",
|
||||
"Mesh",
|
||||
"FlowOnephase"
|
||||
]
|
||||
@ -1,22 +1,12 @@
|
||||
# -*- coding: utf-8 -*-
|
||||
# This file is part of anisotropy.
|
||||
# License: GNU GPL version 3, see the file "LICENSE" for details.
|
||||
|
||||
from peewee import (
|
||||
TextField,
|
||||
ColumnBase,
|
||||
Value,
|
||||
fn,
|
||||
Node,
|
||||
Expression,
|
||||
OP,
|
||||
Field
|
||||
)
|
||||
import json
|
||||
from numpy import ndarray
|
||||
|
||||
import peewee as pw
|
||||
import json
|
||||
|
||||
class ListField(TextField):
|
||||
|
||||
class ListField(pw.TextField):
|
||||
field_type = "list"
|
||||
|
||||
def db_value(self, value):
|
||||
@ -29,88 +19,78 @@ class ListField(TextField):
|
||||
try:
|
||||
pval.append(float(entry))
|
||||
|
||||
except:
|
||||
except Exception:
|
||||
pval.append(entry.strip().replace("'", ""))
|
||||
|
||||
return pval
|
||||
|
||||
"""
|
||||
class JSONField(TextField):
|
||||
# TODO: fix double quotes when use __eq__ in 'where' method
|
||||
field_type = "TEXT"
|
||||
|
||||
def db_value(self, value):
|
||||
if isinstance(value, ndarray):
|
||||
formatted = list(value)
|
||||
|
||||
else:
|
||||
formatted = value
|
||||
|
||||
return json.dumps(formatted)
|
||||
|
||||
def python_value(self, value):
|
||||
if value is not None:
|
||||
return json.loads(value)
|
||||
"""
|
||||
|
||||
class JSONPath(ColumnBase):
|
||||
class JSONPath(pw.ColumnBase):
|
||||
def __init__(self, field, path = None):
|
||||
super(JSONPath, self).__init__()
|
||||
|
||||
self._field = field
|
||||
self._path = path or ()
|
||||
|
||||
@property
|
||||
def path(self):
|
||||
return Value('$%s' % ''.join(self._path))
|
||||
return pw.Value('$%s' % ''.join(self._path))
|
||||
|
||||
def __getitem__(self, idx):
|
||||
if isinstance(idx, int):
|
||||
item = '[%s]' % idx
|
||||
|
||||
else:
|
||||
item = '.%s' % idx
|
||||
|
||||
return JSONPath(self._field, self._path + (item,))
|
||||
|
||||
def set(self, value, as_json = None):
|
||||
if as_json or isinstance(value, (list, dict)):
|
||||
value = fn.json(self._field._json_dumps(value))
|
||||
return fn.json_set(self._field, self.path, value)
|
||||
value = pw.fn.json(self._field._json_dumps(value))
|
||||
|
||||
return pw.fn.json_set(self._field, self.path, value)
|
||||
|
||||
def update(self, value):
|
||||
return self.set(fn.json_patch(self, self._field._json_dumps(value)))
|
||||
return self.set(pw.fn.json_patch(self, self._field._json_dumps(value)))
|
||||
|
||||
def remove(self):
|
||||
return fn.json_remove(self._field, self.path)
|
||||
return pw.fn.json_remove(self._field, self.path)
|
||||
|
||||
def json_type(self):
|
||||
return fn.json_type(self._field, self.path)
|
||||
return pw.fn.json_type(self._field, self.path)
|
||||
|
||||
def length(self):
|
||||
return fn.json_array_length(self._field, self.path)
|
||||
return pw.fn.json_array_length(self._field, self.path)
|
||||
|
||||
def children(self):
|
||||
return fn.json_each(self._field, self.path)
|
||||
return pw.fn.json_each(self._field, self.path)
|
||||
|
||||
def tree(self):
|
||||
return fn.json_tree(self._field, self.path)
|
||||
return pw.fn.json_tree(self._field, self.path)
|
||||
|
||||
def __sql__(self, ctx):
|
||||
return ctx.sql(fn.json_extract(self._field, self.path)
|
||||
if self._path else self._field)
|
||||
return ctx.sql(
|
||||
pw.fn.json_extract(self._field, self.path)
|
||||
if self._path else self._field
|
||||
)
|
||||
|
||||
|
||||
class JSONField(TextField):
|
||||
class JSONField(pw.TextField):
|
||||
field_type = 'TEXT'
|
||||
unpack = False
|
||||
|
||||
def __init__(self, json_dumps = None, json_loads = None, **kwargs):
|
||||
super(JSONField, self).__init__(**kwargs)
|
||||
|
||||
self._json_dumps = json_dumps or json.dumps
|
||||
self._json_loads = json_loads or json.loads
|
||||
super(JSONField, self).__init__(**kwargs)
|
||||
|
||||
def python_value(self, value):
|
||||
if value is not None:
|
||||
try:
|
||||
return json.loads(value)
|
||||
|
||||
except (TypeError, ValueError):
|
||||
return value
|
||||
|
||||
@ -119,23 +99,27 @@ class JSONField(TextField):
|
||||
if isinstance(value, ndarray):
|
||||
value = list(value)
|
||||
|
||||
if not isinstance(value, Node):
|
||||
if not isinstance(value, pw.Node):
|
||||
value = json.dumps(value)
|
||||
|
||||
return value
|
||||
|
||||
def _e(op):
|
||||
def inner(self, rhs):
|
||||
if isinstance(rhs, (list, dict)):
|
||||
rhs = Value(rhs, converter=self.db_value, unpack=False)
|
||||
return Expression(self, op, rhs)
|
||||
rhs = pw.Value(rhs, converter = self.db_value, unpack = False)
|
||||
|
||||
return pw.Expression(self, op, rhs)
|
||||
|
||||
return inner
|
||||
__eq__ = _e(OP.EQ)
|
||||
__ne__ = _e(OP.NE)
|
||||
__gt__ = _e(OP.GT)
|
||||
__ge__ = _e(OP.GTE)
|
||||
__lt__ = _e(OP.LT)
|
||||
__le__ = _e(OP.LTE)
|
||||
__hash__ = Field.__hash__
|
||||
|
||||
__eq__ = _e(pw.OP.EQ)
|
||||
__ne__ = _e(pw.OP.NE)
|
||||
__gt__ = _e(pw.OP.GT)
|
||||
__ge__ = _e(pw.OP.GTE)
|
||||
__lt__ = _e(pw.OP.LT)
|
||||
__le__ = _e(pw.OP.LTE)
|
||||
__hash__ = pw.Field.__hash__
|
||||
|
||||
def __getitem__(self, item):
|
||||
return JSONPath(self)[item]
|
||||
@ -150,10 +134,10 @@ class JSONField(TextField):
|
||||
return JSONPath(self).remove()
|
||||
|
||||
def json_type(self):
|
||||
return fn.json_type(self)
|
||||
return pw.fn.json_type(self)
|
||||
|
||||
def length(self):
|
||||
return fn.json_array_length(self)
|
||||
return pw.fn.json_array_length(self)
|
||||
|
||||
def children(self):
|
||||
"""
|
||||
@ -170,8 +154,7 @@ class JSONField(TextField):
|
||||
json JSON hidden (1st input parameter to function)
|
||||
root TEXT hidden (2nd input parameter, path at which to start)
|
||||
"""
|
||||
return fn.json_each(self)
|
||||
return pw.fn.json_each(self)
|
||||
|
||||
def tree(self):
|
||||
return fn.json_tree(self)
|
||||
|
||||
return pw.fn.json_tree(self)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user