diff --git a/chord_drs/db.py b/chord_drs/db.py index 2a55255..84bd93b 100644 --- a/chord_drs/db.py +++ b/chord_drs/db.py @@ -1,5 +1,7 @@ from flask_sqlalchemy import SQLAlchemy +from .models import Base + __all__ = ["db"] -db = SQLAlchemy() +db = SQLAlchemy(model_class=Base) diff --git a/chord_drs/models.py b/chord_drs/models.py index b874b66..9407290 100644 --- a/chord_drs/models.py +++ b/chord_drs/models.py @@ -2,38 +2,47 @@ from flask import current_app from hashlib import sha256 from pathlib import Path +from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, String from sqlalchemy.sql import func -from sqlalchemy.orm import relationship +from sqlalchemy.orm import declarative_base, relationship from werkzeug.utils import secure_filename from urllib.parse import urlparse from uuid import uuid4 from .backend import get_backend from .backends.minio import MinioBackend -from .db import db from .utils import drs_file_checksum +__all__ = [ + "Base", + "DrsMixin", + "DrsBlob", + "DrsBundle", +] + +Base = declarative_base() + class DrsMixin: # IDs (PKs) must remain outside the mixin! - created = db.Column(db.DateTime, server_default=func.now()) - checksum = db.Column(db.String(64), nullable=False) - size = db.Column(db.Integer, default=0) - name = db.Column(db.String(250), nullable=True) - description = db.Column(db.String(1000), nullable=True) + created = Column(DateTime, server_default=func.now()) + checksum = Column(String(64), nullable=False) + size = Column(Integer, default=0) + name = Column(String(250), nullable=True) + description = Column(String(1000), nullable=True) # Permissions/Bento-specific project & dataset tagging for DRS items # TODO: Make some of these not nullable in the future: - project_id = db.Column(db.String(64), nullable=True) # Nullable for backwards-compatibility - dataset_id = db.Column(db.String(64), nullable=True) # Nullable for backwards-compatibility / project-only stuff? - data_type = db.Column(db.String(24), nullable=True) # NULL if multi-data type or something else - public = db.Column(db.Boolean, default=False, nullable=False) # If true, the object is accessible by anyone + project_id = Column(String(64), nullable=True) # Nullable for backwards-compatibility + dataset_id = Column(String(64), nullable=True) # Nullable for backwards-compatibility / project-only stuff? + data_type = Column(String(24), nullable=True) # NULL if multi-data type or something else + public = Column(Boolean, default=False, nullable=False) # If true, the object is accessible by anyone -class DrsBundle(db.Model, DrsMixin): +class DrsBundle(Base, DrsMixin): __tablename__ = "drs_bundle" - id = db.Column(db.String, primary_key=True) - parent_bundle_id = db.Column(db.Integer, db.ForeignKey("drs_bundle.id")) + id = Column(String, primary_key=True) + parent_bundle_id = Column(Integer, ForeignKey("drs_bundle.id")) parent_bundle = relationship("DrsBundle", remote_side=[id]) objects = relationship("DrsBlob", cascade="all, delete-orphan", backref="bundle") @@ -62,12 +71,12 @@ def update_checksum_and_size(self): self.size = total_size -class DrsBlob(db.Model, DrsMixin): +class DrsBlob(Base, DrsMixin): __tablename__ = "drs_object" - id = db.Column(db.String, primary_key=True) - bundle_id = db.Column(db.Integer, db.ForeignKey(DrsBundle.id), nullable=True) - location = db.Column(db.String(500), nullable=False) + id = Column(String, primary_key=True) + bundle_id = Column(Integer, ForeignKey(DrsBundle.id), nullable=True) + location = Column(String(500), nullable=False) def __init__(self, *args, **kwargs): logger = current_app.logger diff --git a/poetry.lock b/poetry.lock index ae1d34b..b8d65d4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,87 +13,87 @@ files = [ [[package]] name = "aiohttp" -version = "3.9.3" +version = "3.9.4" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.8" files = [ - {file = "aiohttp-3.9.3-cp310-cp310-macosx_10_9_universal2.whl", 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