sqlalchemy-oushudb 0.0.1

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Sqlalchemy OushuDB

modified from [sqlalchemy_hawq]https://github.com/bcgsc/sqlalchemy_hawq

• Sqlalchemy OushuDB
  • Getting Started
    • Install (For developers)
    • Run Tests
    • Deploy (For developers)
  • Using in a SQLAlchemy project
    • How to incorporate sqlalchemy-oushudb
    • OushuDB-specific table arguments
    • Example of oushudb table arguments with declarative syntax
  • Using partitions

This is a custom dialect for using SQLAlchemy with a OushuDB database.

It extends the Postgresql dialect.

Features include:

• skip some pg_catalog tables and columns which not exists in gp/oushudb
• OushuDB options for 'CREATE TABLE' statements
• a point class
• a modified 'DELETE' statement for compatibility with SQLAlchemy's test suite

Unless specifically overridden, any functionality in SQLAlchemy's Postgresql dialect is also available. Note that in general, functionality that is available in Postgresql but not in OushuDB has not yet been disabled.

Getting Started

Install (For developers)

clone this repository

git clone [e-mail]:ojuejuno/sqlalchemy_oushudb.git
cd sqlalchemy_oushudb

create a virtual environment

python3 -m venv venv
source venv/bin/activate

install the package and its development dependencies

pip install -e .[dev]

Run Tests

sqlalchemy_oushu incorporates the standard SQLAlchemy test suite as well as some tests of its own. Run them all as follows:

export OUSHUDB_DB_HOST=<host>
export OUSHUDB_DB_PORT=<port>
export OUSHUDB_DB_NAME=<test db>
export OUSHUDB_DB_DRIVER=oushudb
export OUSHUDB_DB_USER=<your username>
export OUSHUDB_DB_PASS=<your password>
pytest test

Run only the standard SQLAlchemy test suite:

pytest test --oushudb://username:password@hostname:port/database --sqla-only

Run only the custom sqlalchemy_oushudb tests:

pytest test --oushudb://username:password@hostname:port/database --custom-only

Run only the custom tests that don't require a live db connection:

pytest test --offline-only --disable-asyncio

For tests that use a live db connection, user running the tests must be able to create and drop tables on the db provided. Also, many of the tests require that there are pre-existing schemas 'test_schema' and 'test_schema_2' on the db. The test suite can be run without them but the tests will fail.

See https://github.com/zzzeek/sqlalchemy/blob/master/README.unittests.rst and https://github.com/zzzeek/sqlalchemy/blob/master/README.dialects.rst for more information on test configuration. Note that no default db url is stored in sqlalchemy_oushudb's setup.cfg.

Deploy (For developers)

Create the venv and ensure the latest versions of setuptools and pip are installed:

python3 -m venv venv
source venv/bin/activate
pip install -U setuptools pip

Install sqlalchemy_oushudb for deployment and create the distribution packages:

pip install .[deploy]
python3 setup.py sdist

安装

pip install dist/sqlalchemy_oushudb-0.0.1.tar.gz

If you want, you can now check for any problems in the distribution files:

twine check dist/*

Then:

twine upload dist/* --repository-url http://pyshop.bcgsc.ca/simple/

---

Using in a SQLAlchemy project

How to incorporate sqlalchemy-oushudb

Add sqlalchemy_oushudb to your dependencies and install.

pip install sqlalchemy_oushudb

Then the plugin can be used like any other engine

from sqlalchemy import create_engine

engine = create_engine('oushudb://USERNAME:[e-mail]:5432/test_refactor/')

For instructions on how to use the SQLAlchemy engine, see https://docs.sqlalchemy.org/en/20/core/engines.html.

OushuDB-specific table arguments

OushuDB specific table arguments are also supported (Not all features are supported yet)

Argument	Type	Example	Notes
oushudb_distributed_by	str	'column_name'
oushudb_partition_by	RangePartition or ListPartition	ListPartition('chrom', {'chr1': '1', 'chr2':'2', 'chr3':'3'}, [RangeSubpartition('year', 2002, 2012, 1), RangeSubpartition('month', 1, 13, 1),])	Does not currently support range partitioning on dates
oushudb_apppendonly	bool	True
oushudb_orientation	str	'ROW'	expects one of {'ROW', 'PARQUET'}
oushudb_compresstype	str	'ZLIB'	expects one of {'ZLIB', 'SNAPPY', 'GZIP', 'NONE'}
oushudb_compresslevel	int	0	expects an integer between 0-9
oushudb_bucketnum	int	6	expects an integer between 0 and default_hash_table_bucket_number

Example of oushudb table arguments with declarative syntax

from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy import Column, Text

Base = declarative_base()

class ExampleTable(Base):
    __tablename__ = 'example_table'

    __table_args__ = {
        'oushudb_distributed_by': 'attr1'
        'oushudb_appendonly': 'True'
    }

    attr1 = Column(Integer())
    attr2 = Column(Integer())


def main():
    engine = create_engine('oushudb://USERNAME:[e-mail]:5432/test_refactor/')
    engine.create_all()

---

Using partitions

See http://www.oushu.com/docs/oushudb/userguide/data-definition-partition-tables.html for an extended discussion of how partitions work in OushuDB.

Basically, partitioning divides a table into several smaller tables on the value of one or more columns, in order to reduce search time on those columns. The parent table can then be queried/added to without any further reference to the partitions, as OushuDB handles all the parent-partition interactions.

Partition arguments are:

RangePartition(
    column_name=str,
    start=int,
    end=int,
    every=int,
    subpartitions=[])

or

ListPartition(
    column_name=str,
    columns=dict{name_of_partition:value_to_partition_on},
    subpartitions=[])

where 'subpartitions' is an array of RangeSubpartitions and/or ListSubpartitions.

Subpartition arguments are

RangeSubpartition(
    column_name=str,
    start=int,
    end=int,
    every=int)

or

ListSubpartition(
    column_name=str,
    columns=dict{name_of_partition:value_to_partition_on})

Note that the params are the same for the Subpartitions are for the Partitions, except that Subpartitions do not have a nested subpartition array.

Partition level is determined by the order of the subpartitions in the subpartition array.

Using sqlalchemy-oushudb syntax to define a partition:

class MockTable(base):
    __tablename__ = 'MockTable'
    __table_args__ = {
        'oushudb_partition_by': RangePartition(
            'year',
            2009,
            2012,
            1,
            [
                RangeSubpartition(
                    'quarter',
                    1,
                    5,
                    1),
                ListSubpartition(
                    'chrom',
                    {
                        'chr1': '1',
                        'chr2': '2',
                        'chr3': '3'}),
            ],
        )
    }
    id = Column('id', Integer(), primary_key=True, autoincrement=False)
    year = Column('year', Integer())
    quarter = Column('quarter', Integer())
    chrom = Column('chrom', Text())

The SQL output:

'''CREATE TABLE "MockTable" (
	id INTEGER NOT NULL,
	year INTEGER,
	quarter INTEGER,
	chrom TEXT
)
PARTITION BY RANGE (year)
    SUBPARTITION BY RANGE (quarter)
    SUBPARTITION TEMPLATE
    (
        START (1) END (5) EVERY (1),
        DEFAULT SUBPARTITION extra
    )
    SUBPARTITION BY LIST (chrom)
    SUBPARTITION TEMPLATE
    (
        SUBPARTITION chr1 VALUES ('1'),
        SUBPARTITION chr2 VALUES ('2'),
        SUBPARTITION chr3 VALUES ('3'),
        DEFAULT SUBPARTITION other
    )
(
    START (2009) END (2012) EVERY (2),
    DEFAULT PARTITION extra
)'''

The resulting tables:

test_refactor=> \dt
                            List of relations
 Schema |                     Name                      | Type  |  Owner
--------+-----------------------------------------------+-------+---------
 public | MockTable                                     | table | elewis
 public | MockTable_1_prt_2                             | table | elewis
 public | MockTable_1_prt_2_2_prt_2                     | table | elewis
 public | MockTable_1_prt_2_2_prt_2_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_2_2_prt_2_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_2_2_prt_2_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_2_2_prt_2_3_prt_other         | table | elewis
 public | MockTable_1_prt_2_2_prt_3                     | table | elewis
 public | MockTable_1_prt_2_2_prt_3_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_2_2_prt_3_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_2_2_prt_3_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_2_2_prt_3_3_prt_other         | table | elewis
 public | MockTable_1_prt_2_2_prt_4                     | table | elewis
 public | MockTable_1_prt_2_2_prt_4_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_2_2_prt_4_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_2_2_prt_4_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_2_2_prt_4_3_prt_other         | table | elewis
 public | MockTable_1_prt_2_2_prt_5                     | table | elewis
 public | MockTable_1_prt_2_2_prt_5_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_2_2_prt_5_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_2_2_prt_5_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_2_2_prt_5_3_prt_other         | table | elewis
 public | MockTable_1_prt_2_2_prt_extra                 | table | elewis
 public | MockTable_1_prt_2_2_prt_extra_3_prt_chr1      | table | elewis
 public | MockTable_1_prt_2_2_prt_extra_3_prt_chr2      | table | elewis
 public | MockTable_1_prt_2_2_prt_extra_3_prt_chr3      | table | elewis
 public | MockTable_1_prt_2_2_prt_extra_3_prt_other     | table | elewis
 public | MockTable_1_prt_3                             | table | elewis
 public | MockTable_1_prt_3_2_prt_2                     | table | elewis
 public | MockTable_1_prt_3_2_prt_2_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_3_2_prt_2_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_3_2_prt_2_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_3_2_prt_2_3_prt_other         | table | elewis
 public | MockTable_1_prt_3_2_prt_3                     | table | elewis
 public | MockTable_1_prt_3_2_prt_3_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_3_2_prt_3_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_3_2_prt_3_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_3_2_prt_3_3_prt_other         | table | elewis
 public | MockTable_1_prt_3_2_prt_4                     | table | elewis
 public | MockTable_1_prt_3_2_prt_4_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_3_2_prt_4_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_3_2_prt_4_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_3_2_prt_4_3_prt_other         | table | elewis
 public | MockTable_1_prt_3_2_prt_5                     | table | elewis
 public | MockTable_1_prt_3_2_prt_5_3_prt_chr1          | table | elewis
 public | MockTable_1_prt_3_2_prt_5_3_prt_chr2          | table | elewis
 public | MockTable_1_prt_3_2_prt_5_3_prt_chr3          | table | elewis
 public | MockTable_1_prt_3_2_prt_5_3_prt_other         | table | elewis
 public | MockTable_1_prt_3_2_prt_extra                 | table | elewis
 public | MockTable_1_prt_3_2_prt_extra_3_prt_chr1      | table | elewis
 public | MockTable_1_prt_3_2_prt_extra_3_prt_chr2      | table | elewis
 public | MockTable_1_prt_3_2_prt_extra_3_prt_chr3      | table | elewis
 public | MockTable_1_prt_3_2_prt_extra_3_prt_other     | table | elewis
 public | MockTable_1_prt_extra                         | table | elewis
 public | MockTable_1_prt_extra_2_prt_2                 | table | elewis
 public | MockTable_1_prt_extra_2_prt_2_3_prt_chr1      | table | elewis
 public | MockTable_1_prt_extra_2_prt_2_3_prt_chr2      | table | elewis
 public | MockTable_1_prt_extra_2_prt_2_3_prt_chr3      | table | elewis
 public | MockTable_1_prt_extra_2_prt_2_3_prt_other     | table | elewis
 public | MockTable_1_prt_extra_2_prt_3                 | table | elewis
 public | MockTable_1_prt_extra_2_prt_3_3_prt_chr1      | table | elewis
 public | MockTable_1_prt_extra_2_prt_3_3_prt_chr2      | table | elewis
 public | MockTable_1_prt_extra_2_prt_3_3_prt_chr3      | table | elewis
 public | MockTable_1_prt_extra_2_prt_3_3_prt_other     | table | elewis
 public | MockTable_1_prt_extra_2_prt_4                 | table | elewis
 public | MockTable_1_prt_extra_2_prt_4_3_prt_chr1      | table | elewis
 public | MockTable_1_prt_extra_2_prt_4_3_prt_chr2      | table | elewis
 public | MockTable_1_prt_extra_2_prt_4_3_prt_chr3      | table | elewis
 public | MockTable_1_prt_extra_2_prt_4_3_prt_other     | table | elewis
 public | MockTable_1_prt_extra_2_prt_5                 | table | elewis
 public | MockTable_1_prt_extra_2_prt_5_3_prt_chr1      | table | elewis
 public | MockTable_1_prt_extra_2_prt_5_3_prt_chr2      | table | elewis
 public | MockTable_1_prt_extra_2_prt_5_3_prt_chr3      | table | elewis
 public | MockTable_1_prt_extra_2_prt_5_3_prt_other     | table | elewis
 public | MockTable_1_prt_extra_2_prt_extra             | table | elewis
 public | MockTable_1_prt_extra_2_prt_extra_3_prt_chr1  | table | elewis
 public | MockTable_1_prt_extra_2_prt_extra_3_prt_chr2  | table | elewis
 public | MockTable_1_prt_extra_2_prt_extra_3_prt_chr3  | table | elewis
 public | MockTable_1_prt_extra_2_prt_extra_3_prt_other | table | elewis