QuLab 2.0.2__cp310-cp310-macosx_10_9_universal2.whl

qulab/scan/models.py

@@ -0,0 +1,540 @@
+import hashlib
+import pickle
+import time
+from datetime import datetime, timezone
+from functools import singledispatchmethod
+from typing import Optional
+
+from sqlalchemy import (JSON, Column, DateTime, Float, ForeignKey, Integer,
+                        LargeBinary, String, Table, Text, create_engine)
+from sqlalchemy.orm import (backref, declarative_base, relationship,
+                            sessionmaker)
+from sqlalchemy.orm.session import Session
+from waveforms.security import InvalidKey, encryptPassword, verifyPassword
+
+
+def utcnow():
+    return datetime.now(timezone.utc)
+
+
+Base = declarative_base()
+
+# association table
+user_roles = Table('user_roles', Base.metadata,
+                   Column('user_id', ForeignKey('users.id'), primary_key=True),
+                   Column('role_id', ForeignKey('roles.id'), primary_key=True))
+
+record_reports = Table(
+    'record_reports', Base.metadata,
+    Column('record_id', ForeignKey('records.id'), primary_key=True),
+    Column('report_id', ForeignKey('reports.id'), primary_key=True))
+
+comment_tags = Table(
+    'comment_tags', Base.metadata,
+    Column('comment_id', ForeignKey('comments.id'), primary_key=True),
+    Column('tag_id', ForeignKey('tags.id'), primary_key=True))
+
+snapshot_tags = Table(
+    'snapshot_tags', Base.metadata,
+    Column('snapshot_id', ForeignKey('snapshots.id'), primary_key=True),
+    Column('tag_id', ForeignKey('tags.id'), primary_key=True))
+
+record_tags = Table(
+    'record_tags', Base.metadata,
+    Column('record_id', ForeignKey('records.id'), primary_key=True),
+    Column('tag_id', ForeignKey('tags.id'), primary_key=True))
+
+report_tags = Table(
+    'report_tags', Base.metadata,
+    Column('report_id', ForeignKey('reports.id'), primary_key=True),
+    Column('tag_id', ForeignKey('tags.id'), primary_key=True))
+
+sample_tags = Table(
+    'sample_tags', Base.metadata,
+    Column('sample_id', ForeignKey('samples.id'), primary_key=True),
+    Column('tag_id', ForeignKey('tags.id'), primary_key=True))
+
+sample_reports = Table(
+    'sample_reports', Base.metadata,
+    Column('sample_id', ForeignKey('samples.id'), primary_key=True),
+    Column('report_id', ForeignKey('reports.id'), primary_key=True))
+
+sample_records = Table(
+    'sample_records', Base.metadata,
+    Column('sample_id', ForeignKey('samples.id'), primary_key=True),
+    Column('record_id', ForeignKey('records.id'), primary_key=True))
+
+sample_comments = Table(
+    'sample_comments', Base.metadata,
+    Column('sample_id', ForeignKey('samples.id'), primary_key=True),
+    Column('comment_id', ForeignKey('comments.id'), primary_key=True))
+
+sample_transfer_comments = Table(
+    'sample_transfer_comments', Base.metadata,
+    Column('transfer_id', ForeignKey('sample_transfer.id'), primary_key=True),
+    Column('comment_id', ForeignKey('comments.id'), primary_key=True))
+
+report_comments = Table(
+    'report_comments', Base.metadata,
+    Column('report_id', ForeignKey('reports.id'), primary_key=True),
+    Column('comment_id', ForeignKey('comments.id'), primary_key=True))
+
+record_comments = Table(
+    'record_comments', Base.metadata,
+    Column('record_id', ForeignKey('records.id'), primary_key=True),
+    Column('comment_id', ForeignKey('comments.id'), primary_key=True))
+
+
+class Role(Base):
+    __tablename__ = 'roles'
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String)
+
+    users = relationship('User', secondary=user_roles, back_populates='roles')
+
+    def __repr__(self):
+        return f"Role(name='{self.name}')"
+
+
+class User(Base):
+    __tablename__ = 'users'
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String, unique=True)
+    hashed_password = Column(LargeBinary(64))
+    fullname = Column(String)
+
+    roles = relationship('Role', secondary=user_roles, back_populates='users')
+    attachments = relationship('Attachment', back_populates='user')
+    comments = relationship('Comment', back_populates='user')
+
+    def setPassword(self, password):
+        self.hashed_password = encryptPassword(password)
+
+    def verify(self, password):
+        try:
+            verifyPassword(password, self.hashed_password)
+            return True
+        except InvalidKey:
+            return False
+
+    def __repr__(self):
+        return f"User(name='{self.name}')"
+
+
+class ParameterEdge(Base):
+    __tablename__ = 'parameter_edges'
+    parent_id = Column(ForeignKey('parameters.id'), primary_key=True)
+    child_id = Column(ForeignKey('parameters.id'), primary_key=True)
+    key = Column(String(50), primary_key=True)
+
+
+class Parameter(Base):
+    __tablename__ = 'parameters'
+
+    id = Column(Integer, primary_key=True)
+    type = Column(String)
+    unit = Column(String)
+    integer = Column(Integer)
+    real = Column(Float)
+    imag = Column(Float)
+    string = Column(String)
+    buff = Column(LargeBinary)
+
+    children = relationship("ParameterEdge",
+                            foreign_keys=[ParameterEdge.parent_id],
+                            backref="parent")
+    parents = relationship("ParameterEdge",
+                           foreign_keys=[ParameterEdge.child_id],
+                           backref="child")
+
+    @property
+    def value(self):
+        if self.type == 'integer':
+            return self.integer
+        elif self.type == 'real':
+            return self.real
+        elif self.type == 'complex':
+            return self.real + 1j * self.imag
+        elif self.type == 'string':
+            return self.string
+        elif self.type == 'buffer':
+            return self.buff
+        elif self.type == 'boolean':
+            return self.integer == 1
+        elif self.type is None or self.type == 'none':
+            return None
+        elif self.type == 'tree':
+            return self.export()
+        else:
+            return pickle.loads(self.buff)
+
+    @value.setter
+    def value(self, value):
+        self._set_value(value)
+
+    @singledispatchmethod
+    def _set_value(self, value):
+        self.buff = pickle.dumps(value)
+        self.type = 'pickle'
+
+    @_set_value.register
+    def _(self, value: int):
+        self.integer = value
+        self.type = 'integer'
+
+    @_set_value.register
+    def _(self, value: bool):
+        self.integer = int(value)
+        self.type = 'boolean'
+
+    @_set_value.register
+    def _(self, value: float):
+        self.real = value
+        self.type = 'real'
+
+    @_set_value.register
+    def _(self, value: complex):
+        self.real = value.real
+        self.imag = value.imag
+        self.type = 'complex'
+
+    @_set_value.register
+    def _(self, value: str):
+        self.string = value
+        self.type = 'string'
+
+    @_set_value.register
+    def _(self, value: bytes):
+        self.buff = value
+        self.type = 'buffer'
+
+    @_set_value.register
+    def _(self, value: None):
+        self.type = 'none'
+
+    def export(self):
+        if self.type == 'tree':
+            return {a.key: a.child.export() for a in self.children}
+        else:
+            return self.value
+
+
+class Snapshot(Base):
+    __tablename__ = 'snapshots'
+
+    id = Column(Integer, primary_key=True)
+    root_id = Column(ForeignKey('parameters.id'))
+    previous_id = Column(Integer, ForeignKey('snapshots.id'))
+
+    followers = relationship("Snapshot",
+                             backref=backref('previous', remote_side=[id]))
+
+    root = relationship('Parameter')
+    tags = relationship('Tag',
+                        secondary=snapshot_tags,
+                        back_populates='snapshots')
+
+    def export(self):
+        return self.root.export()
+
+
+class ReportParameters(Base):
+    __tablename__ = 'report_parameters'
+    parent_id = Column(ForeignKey('reports.id'), primary_key=True)
+    child_id = Column(ForeignKey('parameters.id'), primary_key=True)
+    key = Column(String(50), primary_key=True)
+
+    parameter = relationship('Parameter')
+
+    @property
+    def value(self):
+        return self.parameter.value
+
+
+class Tag(Base):
+    __tablename__ = 'tags'
+
+    id = Column(Integer, primary_key=True)
+    text = Column(String, unique=True)
+
+    comments = relationship('Comment',
+                            secondary=comment_tags,
+                            back_populates='tags')
+    records = relationship('Record',
+                           secondary=record_tags,
+                           back_populates='tags')
+    reports = relationship('Report',
+                           secondary=report_tags,
+                           back_populates='tags')
+    samples = relationship('Sample',
+                           secondary=sample_tags,
+                           back_populates='tags')
+    snapshots = relationship('Snapshot',
+                             secondary=snapshot_tags,
+                             back_populates='tags')
+
+    def __init__(self, text) -> None:
+        super().__init__()
+        self.text = text
+
+    def __repr__(self):
+        return f"Tag('{self.text}')"
+
+
+class Comment(Base):
+    __tablename__ = 'comments'
+
+    id = Column(Integer, primary_key=True)
+    text = Column(String)
+    user_id = Column(Integer, ForeignKey('users.id'))
+    ctime = Column(DateTime, default=utcnow)
+    mtime = Column(DateTime, default=utcnow)
+    atime = Column(DateTime, default=utcnow)
+    parent_id = Column(Integer, ForeignKey('comments.id'))
+
+    replies = relationship("Comment", lazy="joined", join_depth=2)
+    user = relationship('User', back_populates='comments')
+    tags = relationship('Tag',
+                        secondary=comment_tags,
+                        back_populates='comments')
+    attachments = relationship('Attachment', back_populates='comment')
+
+
+class Attachment(Base):
+    __tablename__ = 'attachments'
+
+    id = Column(Integer, primary_key=True)
+    filename = Column(String)
+    mime_type = Column(String, default='application/octet-stream')
+    user_id = Column(Integer, ForeignKey('users.id'))
+    comment_id = Column(Integer, ForeignKey('comments.id'))
+    ctime = Column(DateTime, default=utcnow)
+    mtime = Column(DateTime, default=utcnow)
+    atime = Column(DateTime, default=utcnow)
+    size = Column(Integer)
+    sha1 = Column(String)
+    description = Column(Text)
+
+    user = relationship('User', back_populates='attachments')
+    comment = relationship('Comment', back_populates='attachments')
+
+
+class InputText(Base):
+    __tablename__ = 'inputs'
+
+    id = Column(Integer, primary_key=True)
+    hash = Column(LargeBinary(20))
+    text_field = Column(Text, unique=True)
+
+    @property
+    def text(self):
+        return self.text_field
+
+    @text.setter
+    def text(self, text):
+        self.hash = hashlib.sha1(text.encode('utf-8')).digest()
+        self.text_field = text
+
+    def __repr__(self) -> str:
+        return self.text
+
+
+class Cell(Base):
+    __tablename__ = 'cells'
+
+    id = Column(Integer, primary_key=True)
+    notebook_id = Column(Integer, ForeignKey("notebooks.id"))
+    index = Column(Integer)
+    ctime = Column(DateTime, default=utcnow)
+    ftime = Column(DateTime, default=utcnow)
+    input_id = Column(Integer, ForeignKey("inputs.id"))
+
+    notebook = relationship("Notebook", back_populates="cells")
+    input = relationship("InputText")
+
+    def __repr__(self) -> str:
+        return str(f"Cell(index={self.index}, input='{self.input}')")
+
+
+class Notebook(Base):
+    __tablename__ = 'notebooks'
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String)
+    ctime = Column(DateTime, default=utcnow)
+    atime = Column(DateTime, default=utcnow)
+
+    cells = relationship("Cell",
+                         order_by=Cell.index,
+                         back_populates="notebook")
+
+
+class Sample(Base):
+    __tablename__ = 'samples'
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String)
+
+    account_id = Column(Integer, ForeignKey("sample_accounts.id"))
+
+    tags = relationship("Tag", secondary=sample_tags, back_populates="samples")
+    records = relationship("Record",
+                           secondary=sample_records,
+                           back_populates="samples")
+    reports = relationship("Report",
+                           secondary=sample_reports,
+                           back_populates="samples")
+    transfers = relationship("SampleTransfer",
+                             order_by="SampleTransfer.ctime",
+                             back_populates="sample")
+    account = relationship("SampleAccount", back_populates="samples")
+    comments = relationship("Comment", secondary=sample_comments)
+
+
+class SampleAccountType(Base):
+    __tablename__ = 'sample_account_types'
+    id = Column(Integer, primary_key=True)
+    name = Column(String)
+    description = Column(String)
+
+    accounts = relationship("SampleAccount", back_populates="type")
+
+
+class SampleAccount(Base):
+    __tablename__ = 'sample_accounts'
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String)
+    type_id = Column(Integer, ForeignKey("sample_account_types.id"))
+    description = Column(String)
+
+    type = relationship("SampleAccountType", back_populates="accounts")
+
+    samples = relationship("Sample", back_populates="account")
+
+
+class SampleTransfer(Base):
+    __tablename__ = 'sample_transfer'
+
+    id = Column(Integer, primary_key=True)
+    sample_id = Column(Integer, ForeignKey("samples.id"))
+    user_id = Column(Integer, ForeignKey("users.id"))
+    ctime = Column(DateTime, default=utcnow)
+    debtor_id = Column(Integer, ForeignKey("sample_accounts.id"))
+    creditor_id = Column(Integer, ForeignKey("sample_accounts.id"))
+
+    user = relationship("User")
+    sample = relationship("Sample", back_populates="transfers")
+    debtor = relationship("SampleAccount", foreign_keys=[debtor_id])
+    creditor = relationship("SampleAccount", foreign_keys=[creditor_id])
+    comments = relationship("Comment", secondary=sample_transfer_comments)
+
+
+class Record(Base):
+    __tablename__ = 'records'
+
+    id = Column(Integer, primary_key=True)
+    ctime = Column(DateTime, default=utcnow)
+    mtime = Column(DateTime, default=utcnow)
+    atime = Column(DateTime, default=utcnow)
+    user_id = Column(Integer, ForeignKey('users.id'))
+    parent_id = Column(Integer, ForeignKey('records.id'))
+    cell_id = Column(Integer, ForeignKey('cells.id'))
+
+    app = Column(String)
+    file = Column(String)
+    key = Column(String)
+    config = Column(JSON)
+    task_hash = Column(LargeBinary(32))
+
+    parent = relationship("Record",
+                          remote_side=[id],
+                          back_populates="children")
+    children = relationship("Record",
+                            remote_side=[parent_id],
+                            back_populates="parent")
+
+    user = relationship("User")
+    samples = relationship("Sample",
+                           secondary=sample_records,
+                           back_populates="records")
+    cell = relationship("Cell")
+
+    reports = relationship('Report',
+                           secondary=record_reports,
+                           back_populates='records')
+    tags = relationship('Tag', secondary=record_tags, back_populates='records')
+    comments = relationship('Comment', secondary=record_comments)
+
+
+class Report(Base):
+    __tablename__ = 'reports'
+
+    id = Column(Integer, primary_key=True)
+    ctime = Column(DateTime, default=utcnow)
+    mtime = Column(DateTime, default=utcnow)
+    atime = Column(DateTime, default=utcnow)
+    user_id = Column(Integer, ForeignKey('users.id'))
+
+    category = Column(String)
+    title = Column(String)
+    content = Column(Text)
+    file = Column(String)
+    key = Column(String)
+    task_hash = Column(LargeBinary(32))
+
+    user = relationship("User")
+    samples = relationship("Sample",
+                           secondary=sample_reports,
+                           back_populates="reports")
+
+    records = relationship('Record',
+                           secondary=record_reports,
+                           back_populates='reports')
+
+    tags = relationship('Tag', secondary=report_tags, back_populates='reports')
+    comments = relationship('Comment', secondary=report_comments)
+    _parameters = relationship('ReportParameters')
+
+
+def create_tables(engine, tables_only=False):
+    Base.metadata.create_all(engine)
+    if tables_only:
+        return
+
+    sys_role = Role(name='sys')
+    kernel = User(name='BIG BROTHER')
+    kernel.roles.append(sys_role)
+
+    root_role = Role(name='root')
+    admin_role = Role(name='admin')
+    root_user = User(name='root')
+    root_user.setPassword('123')
+    root_user.roles.append(root_role)
+    root_user.roles.append(admin_role)
+
+    guest_role = Role(name='guest')
+    guest_user = User(name='guest')
+    guest_user.setPassword('')
+    guest_user.roles.append(guest_role)
+
+    t1 = SampleAccountType(name='factory')
+    t2 = SampleAccountType(name='destroyed')
+    t3 = SampleAccountType(name='storage')
+    t4 = SampleAccountType(name='fridge')
+    a = SampleAccount(name='destroyed')
+    a.type = t2
+
+    Session = sessionmaker(bind=engine)
+    session = Session()
+
+    session.add(root_user)
+    session.add(guest_user)
+    session.add(kernel)
+    session.add_all([t1, t2, t3, t4, a])
+    try:
+        session.commit()
+    except:
+        session.rollback()

qulab/scan/optimize.py

@@ -0,0 +1,69 @@
+from typing import Any, Sequence
+
+import nevergrad as ng
+import numpy as np
+from scipy.optimize import OptimizeResult
+
+
+class NgOptimizer():
+
+    def __init__(self, variables, **kwds):
+        self._all_x, self._all_y = [], []
+        self.config = {
+            'method': 'TBPSA',
+            'budget': 100,
+        }
+        self.config.update(kwds)
+        instrum = []
+        self.dimensions = variables
+        for space in variables:
+
+            if space.transform_ == "normalize":
+                instrum.append(ng.p.Scalar(init=0.5, lower=0, upper=1))
+            else:
+                if space.prior == "log-uniform":
+                    instrum.append(
+                        ng.p.Log(init=None,
+                                 exponent=space.base,
+                                 lower=space.low,
+                                 upper=space.high))
+                else:
+                    instrum.append(
+                        ng.p.Scalar(init=None,
+                                    lower=space.low,
+                                    upper=space.high))
+        self.instrum = ng.p.Instrumentation(*instrum)
+        self.opt = getattr(ng.optimizers,
+                           self.config['method'])(self.instrum,
+                                                  budget=self.config['budget'])
+
+    def ask(self):
+        tmp = self.opt.ask()
+        return [
+            space.inverse_transform(x)
+            for x, space in zip(tmp.args, self.dimensions)
+        ]
+
+    def tell(self, suggested: Sequence, value: Any):
+        self._all_x.append(suggested)
+        self._all_y.append(value)
+        suggested = [
+            space.transform(x) for x, space in zip(suggested, self.dimensions)
+        ]
+        self.opt.suggest(*suggested)
+        x = self.opt.ask()
+        self.opt.tell(x, value)
+
+    def get_result(self, history: bool = False) -> OptimizeResult:
+        recommendation = self.opt.recommend()
+        ret = OptimizeResult({
+            'x': [
+                space.inverse_transform(x)
+                for x, space in zip(recommendation.args, self.dimensions)
+            ]
+        })
+        if history:
+            ret.x_iters = self._all_x
+            ret.func_vals = self._all_y
+        ret.fun = recommendation.value
+        return ret