Question

我正在使用SQLalchemy和automap以及由我无法控制的程序生成的一系列SQLite数据库。但是，我需要扩展数据库以提供其他功能，因此我使用SQLalchemy ORM修改此数据库并使用automap访问我没有更改的表和列。

类定义（保留在自己的模块中）：

Base = automap_base()

class VariantAssociation(Base):

    __tablename__ = "sample_variant_association"

    vid = Column(Integer, ForeignKey("variants.variant_id"),
                 primary_key=True, index=True)
    sid = Column(Integer, ForeignKey("samples.sample_id"),
                 primary_key=True, index=True)

    vdepth = Column(Integer, index=True)
    valt_depth = Column(Integer, index=True)
    gt = Column(Text)
    gt_type = Column(Integer)
    fraction = Column(Float, index=True)

    variant = relationship("Variant", back_populates="samples")
    sample = relationship("Samples", back_populates="variants")


class Variant(Base):

    __tablename__ = "variants"

    variant_id = Column(Integer, primary_key=True)
    info = deferred(Column(LargeBinary))

    samples = relationship("VariantAssociation",
                           back_populates="variant")

    compressed = False

    _gt_alt_depths = None
    _gt_depths = None
    _gts = None
    _gt_types = None

    def decompress(self, compressed=False):

        if compressed:
            unpack = snappy_unpack_blob
        else:
            unpack = unpack_blob

        self._gt_alt_depths = unpack(self.gt_alt_depths)
        self._gt_depths = unpack(self.gt_depths)
        self._gts = unpack(self.gts)
        self._gt_types = unpack(self.gt_types)


    def __repr__(self):

        data = "<Variant {chrom}:{start}-{end} {gene} {ref}/{alt} {type}>"

        return data.format(chrom=self.chrom,
                           start=self.start,
                           end=self.end,
                           gene=self.gene,
                           ref=self.ref,
                           alt=self.alt,
                           type=self.type)

    @property
    def alt_depths(self):
        return self._gt_alt_depths

    @property
    def depths(self):
        return self._gt_depths

    @property
    def genotypes(self):
        return self._gts

    @property
    def genotype_types(self):
        return self._gt_types


class Samples(Base):

    __tablename__ = "samples"

    sample_id = Column(Integer, primary_key=True, index=True)
    name = Column(Text, index=True)
    variants = relationship("VariantAssociation",
                            back_populates="sample")


class DataMigration(Base):

    __tablename__ = "datamigration"
    done = Column(Boolean, primary_key=True)

然后我用这种方法加载数据库（在一个不同的函数中，从定义表的位置导入Base）：

engine = create_engine("sqlite:///{}".format(database),
                           poolclass=StaticPool,
                           echo=echo)

# Create association table if not present
VariantAssociation.__table__.create(bind=engine, checkfirst=True)
DataMigration.__table__.create(bind=engine, checkfirst=True)

Base.prepare(engine, reflect=True)
session = sessionmaker(bind=engine)()

但是，如果我加载两个数据库，第一次泄漏到后续运行中会发生什么：

db = load_database("file1.db") # All right
db2 = load_database("file2.db") # Throws exception

有问题的例外是：

io.py in load_database(database)
150 
151     # Create association table if not present
--> 152     VariantAssociation.__table__.create(bind=engine, checkfirst=True)
153     DataMigration.__table__.create(bind=engine, checkfirst=True)
154 
[cut exception all into SQLalchemy internals]
OperationalError: (sqlite3.OperationalError) index ix_sample_variant_association_valt_depth already exists [SQL: 'CREATE INDEX ix_sample_variant_association_valt_depth ON sample_variant_association (valt_depth)']

如果我在一个单独的会话中加载数据库，则不会发生这种情况，因此db的某个状态正在泄漏到db2。

确保每个加载的数据库ORM独立的最佳方法是什么？

编辑：更多调试显示CREATE INDEX被使用了两次：

2017-09-15 15:18:00,284 INFO sqlalchemy.engine.base.Engine ()
2017-09-15 15:18:00,417 INFO sqlalchemy.engine.base.Engine COMMIT
2017-09-15 15:18:00,418 INFO sqlalchemy.engine.base.Engine CREATE INDEX 
ix_sample_variant_association_valt_depth ON sample_variant_association 
(valt_depth)
2017-09-15 15:18:00,418 INFO sqlalchemy.engine.base.Engine ()
2017-09-15 15:18:00,550 INFO sqlalchemy.engine.base.Engine COMMIT
2017-09-15 15:18:00,551 INFO sqlalchemy.engine.base.Engine CREATE INDEX 
ix_sample_variant_association_valt_depth ON sample_variant_association 
(valt_depth)

SQLalchemy - 会话和多个数据库尝试两次创建索引

0 个答案: