6a0953c913
Updated relationships for beamtime in models to support many-to-many associations with pucks, samples, and dewars. Refactored API endpoints to accommodate these changes, ensuring accurate assignment and retrieval of data. Improved sample data generation logic and incremented the application version for the new updates.
375 lines
13 KiB
Python
375 lines
13 KiB
Python
from sqlalchemy import (
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Column,
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Integer,
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String,
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Date,
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ForeignKey,
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JSON,
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DateTime,
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Boolean,
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func,
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Enum,
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Table,
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)
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from sqlalchemy.orm import relationship
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from .database import Base
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from datetime import datetime
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import enum
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dewar_beamtime_association = Table(
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"dewar_beamtime_association",
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Base.metadata,
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Column("dewar_id", Integer, ForeignKey("dewars.id")),
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Column("beamtime_id", Integer, ForeignKey("beamtimes.id")),
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)
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puck_beamtime_association = Table(
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"puck_beamtime_association",
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Base.metadata,
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Column("puck_id", Integer, ForeignKey("pucks.id")),
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Column("beamtime_id", Integer, ForeignKey("beamtimes.id")),
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)
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sample_beamtime_association = Table(
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"sample_beamtime_association",
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Base.metadata,
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Column("sample_id", Integer, ForeignKey("samples.id")),
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Column("beamtime_id", Integer, ForeignKey("beamtimes.id")),
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)
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class Shipment(Base):
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__tablename__ = "shipments"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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pgroups = Column(String(255), nullable=False)
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shipment_name = Column(String(255), index=True)
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shipment_date = Column(Date, nullable=True)
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shipment_status = Column(String(255), nullable=True)
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comments = Column(String(200), nullable=True)
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contact_id = Column(Integer, ForeignKey("contacts.id"), nullable=False)
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return_address_id = Column(Integer, ForeignKey("addresses.id"), nullable=False)
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proposal_id = Column(Integer, ForeignKey("proposals.id"), nullable=True)
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contact = relationship("Contact", back_populates="shipments")
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return_address = relationship("Address", back_populates="shipments")
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proposal = relationship("Proposal", back_populates="shipments")
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dewars = relationship("Dewar", back_populates="shipment")
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class Contact(Base):
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__tablename__ = "contacts"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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status = Column(String(255), default="active")
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pgroups = Column(String(255), nullable=False)
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firstname = Column(String(255), nullable=False)
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lastname = Column(String(255))
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phone_number = Column(String(255))
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email = Column(String(255))
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shipments = relationship("Shipment", back_populates="contact")
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class LocalContact(Base):
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__tablename__ = "local_contacts"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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status = Column(String(255), default="active")
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firstname = Column(String(255), nullable=False)
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lastname = Column(String(255), nullable=False)
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phone_number = Column(String(255), nullable=False)
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email = Column(String(255), nullable=False)
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class Address(Base):
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__tablename__ = "addresses"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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status = Column(String(255), default="active")
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pgroups = Column(String(255), nullable=False)
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street = Column(String(255), nullable=False)
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house_number = Column(String(255), nullable=True)
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city = Column(String(255), nullable=False)
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state = Column(String(255), nullable=True)
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zipcode = Column(String(255), nullable=False)
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country = Column(String(255), nullable=False)
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shipments = relationship("Shipment", back_populates="return_address")
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class DewarType(Base):
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__tablename__ = "dewar_types"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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dewar_type = Column(String(255), unique=True, index=True)
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serial_numbers = relationship("DewarSerialNumber", back_populates="dewar_type")
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class DewarSerialNumber(Base):
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__tablename__ = "dewar_serial_numbers"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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serial_number = Column(String(255), index=True)
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dewar_type_id = Column(Integer, ForeignKey("dewar_types.id"))
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dewar_type = relationship("DewarType", back_populates="serial_numbers")
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class Dewar(Base):
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__tablename__ = "dewars"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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pgroups = Column(String(255), nullable=False)
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dewar_name = Column(String(255), nullable=False)
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created_at = Column(DateTime, default=datetime.now, nullable=False)
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dewar_type_id = Column(Integer, ForeignKey("dewar_types.id"), nullable=True)
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dewar_serial_number_id = Column(
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Integer, ForeignKey("dewar_serial_numbers.id"), nullable=True
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)
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status = Column(String(255), nullable=True)
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unique_id = Column(String(255), unique=True, index=True, nullable=True)
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tracking_number = Column(String(255), nullable=True)
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shipment_id = Column(Integer, ForeignKey("shipments.id"))
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return_address_id = Column(Integer, ForeignKey("addresses.id"))
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contact_id = Column(Integer, ForeignKey("contacts.id"))
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shipment = relationship("Shipment", back_populates="dewars")
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return_address = relationship("Address")
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contact = relationship("Contact")
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pucks = relationship("Puck", back_populates="dewar")
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dewar_type = relationship("DewarType")
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dewar_serial_number = relationship("DewarSerialNumber")
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slot = relationship("Slot", back_populates="dewar")
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events = relationship("LogisticsEvent", back_populates="dewar")
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beamline_location = None
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local_contact_id = Column(Integer, ForeignKey("local_contacts.id"), nullable=True)
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local_contact = relationship("LocalContact")
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beamtimes = relationship(
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"Beamtime", secondary=dewar_beamtime_association, back_populates="dewars"
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)
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@property
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def number_of_pucks(self) -> int:
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return len(self.pucks) if self.pucks else 0
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@property
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def number_of_samples(self) -> int:
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if not self.pucks:
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return 0
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return sum(len(puck.samples) for puck in self.pucks)
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class Proposal(Base):
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__tablename__ = "proposals"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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number = Column(String(255))
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shipments = relationship("Shipment", back_populates="proposal")
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class Puck(Base):
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__tablename__ = "pucks"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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puck_name = Column(String(255), index=True)
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puck_type = Column(String(255))
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puck_location_in_dewar = Column(Integer)
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# Foreign keys and relationships
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dewar_id = Column(Integer, ForeignKey("dewars.id"))
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dewar = relationship("Dewar", back_populates="pucks")
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samples = relationship("Sample", back_populates="puck")
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events = relationship("PuckEvent", back_populates="puck")
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beamtimes = relationship(
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"Beamtime", secondary=puck_beamtime_association, back_populates="pucks"
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)
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class Sample(Base):
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__tablename__ = "samples"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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sample_name = Column(String(255), index=True)
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proteinname = Column(String(255), index=True)
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position = Column(Integer)
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priority = Column(Integer)
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comments = Column(String(255))
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data_collection_parameters = Column(JSON, nullable=True)
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# Foreign keys and relationships
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dewar_id = Column(Integer, ForeignKey("dewars.id"))
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puck_id = Column(Integer, ForeignKey("pucks.id"))
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puck = relationship("Puck", back_populates="samples")
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events = relationship("SampleEvent", back_populates="sample", lazy="joined")
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images = relationship("Image", back_populates="sample", lazy="joined")
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beamtimes = relationship(
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"Beamtime", secondary=sample_beamtime_association, back_populates="samples"
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)
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@property
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def mount_count(self) -> int:
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# Dynamically calculate mount_count
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return len([event for event in self.events if event.event_type == "Mounted"])
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@property
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def unmount_count(self) -> int:
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# Dynamically calculate unmount_count
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return len([event for event in self.events if event.event_type == "Unmounted"])
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class Slot(Base):
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__tablename__ = "slots"
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id = Column(Integer, primary_key=True, index=True)
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qr_code = Column(String(255), unique=True, index=True)
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label = Column(String(255))
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qr_base = Column(String(255), nullable=True)
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occupied = Column(Boolean, default=False)
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needs_refill = Column(Boolean, default=False)
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dewar_unique_id = Column(String(255), ForeignKey("dewars.unique_id"), nullable=True)
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dewar = relationship("Dewar", back_populates="slot")
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events = relationship("LogisticsEvent", back_populates="slot")
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class LogisticsEvent(Base):
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__tablename__ = "logistics_events"
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id = Column(Integer, primary_key=True, index=True)
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dewar_id = Column(Integer, ForeignKey("dewars.id"))
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slot_id = Column(Integer, ForeignKey("slots.id"))
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event_type = Column(String(255), index=True)
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timestamp = Column(DateTime, default=datetime.now)
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dewar = relationship("Dewar", back_populates="events")
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slot = relationship("Slot", back_populates="events")
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class SampleEvent(Base):
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__tablename__ = "sample_events"
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id = Column(Integer, primary_key=True, index=True)
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sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
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event_type = Column(String(255), nullable=False)
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timestamp = Column(DateTime, default=datetime.now)
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images = relationship("Image", back_populates="sample_event")
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sample = relationship("Sample", back_populates="events")
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class PuckEvent(Base):
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__tablename__ = "puck_events"
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id = Column(Integer, primary_key=True, index=True)
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puck_id = Column(Integer, ForeignKey("pucks.id"))
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tell = Column(String(255), nullable=True)
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tell_position = Column(String(255), nullable=True)
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event_type = Column(String(255), index=True)
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timestamp = Column(DateTime, default=datetime.now)
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puck = relationship("Puck", back_populates="events")
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SHIFT_CHOICES = ("morning", "afternoon", "night")
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class Beamtime(Base):
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__tablename__ = "beamtimes"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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pgroups = Column(String(255), nullable=False)
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shift = Column(Enum(*SHIFT_CHOICES, name="shift_enum"), nullable=False, index=True)
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beamtime_name = Column(String(255), index=True)
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beamline = Column(String(255), nullable=True)
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start_date = Column(Date, nullable=True)
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end_date = Column(Date, nullable=True)
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status = Column(String(255), nullable=True)
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comments = Column(String(200), nullable=True)
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proposal_id = Column(Integer, ForeignKey("proposals.id"), nullable=True)
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local_contact_id = Column(Integer, ForeignKey("local_contacts.id"), nullable=False)
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local_contact = relationship("LocalContact")
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dewars = relationship(
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"Dewar", secondary=dewar_beamtime_association, back_populates="beamtimes"
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)
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pucks = relationship(
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"Puck", secondary=puck_beamtime_association, back_populates="beamtimes"
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)
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samples = relationship(
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"Sample", secondary=sample_beamtime_association, back_populates="beamtimes"
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)
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class Image(Base):
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__tablename__ = "images"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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pgroup = Column(String(255), nullable=False)
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comment = Column(String(200), nullable=True)
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filepath = Column(String(255), nullable=False)
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status = Column(String(255), nullable=True)
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sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
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sample_event_id = Column(Integer, ForeignKey("sample_events.id"), nullable=False)
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sample = relationship("Sample", back_populates="images")
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sample_event = relationship("SampleEvent", back_populates="images")
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class ExperimentParameters(Base):
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__tablename__ = "experiment_parameters"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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run_number = Column(Integer, nullable=False)
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type = Column(String(255), nullable=False)
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beamline_parameters = Column(JSON, nullable=True)
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dataset = Column(JSON, nullable=True)
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sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
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class Results(Base):
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__tablename__ = "results"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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status = Column(String(255), nullable=False)
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result = Column(JSON, nullable=False) # store the full result object as JSON
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sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
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run_id = Column(Integer, ForeignKey("experiment_parameters.id"), nullable=False)
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# optional relationships if you wish to query easily
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# sample = relationship("SampleModel", backref="results")
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# experiment_parameters = relationship("ExperimentParametersModel",
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# backref="results")
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# method = Column(String(255), nullable=False)
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# #resolution: Column(Float(255), nullable=False)
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# unit_cell: str
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# spacegroup: str
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# rmerge: float
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# rmeas: float
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# isig: float
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# cc: float
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# cchalf: float
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# completeness: float
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# multiplicity: float
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# nobs: int
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# total_refl: int
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# unique_refl: int
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# #comments: Optional[constr(max_length=200)] = None
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class JobStatus(str, enum.Enum):
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TO_DO = "to_do"
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SUBMITTED = "submitted"
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DONE = "done"
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TO_CANCEL = "to_cancel"
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CANCELLED = "cancelled"
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FAILED = "failed"
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class Jobs(Base):
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__tablename__ = "jobs"
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id = Column(Integer, primary_key=True, index=True)
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sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
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run_id = Column(Integer, ForeignKey("experiment_parameters.id"), nullable=False)
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status = Column(String, nullable=False)
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experiment_parameters = relationship(ExperimentParameters)
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created_at = Column(DateTime, server_default=func.now())
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updated_at = Column(DateTime, onupdate=func.now())
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slurm_id = Column(Integer, nullable=True)
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