Source code for dask.dataframe.io.sql

import numpy as np
import pandas as pd

import dask
from dask.delayed import tokenize

from ... import delayed
from .. import methods
from .io import from_delayed, from_pandas


[docs]def read_sql_table( table, uri, index_col, divisions=None, npartitions=None, limits=None, columns=None, bytes_per_chunk="256 MiB", head_rows=5, schema=None, meta=None, engine_kwargs=None, **kwargs, ): """ Create dataframe from an SQL table. If neither divisions or npartitions is given, the memory footprint of the first few rows will be determined, and partitions of size ~256MB will be used. Parameters ---------- table : string or sqlalchemy expression Select columns from here. uri : string Full sqlalchemy URI for the database connection index_col : string Column which becomes the index, and defines the partitioning. Should be a indexed column in the SQL server, and any orderable type. If the type is number or time, then partition boundaries can be inferred from npartitions or bytes_per_chunk; otherwide must supply explicit ``divisions=``. ``index_col`` could be a function to return a value, e.g., ``sql.func.abs(sql.column('value')).label('abs(value)')``. ``index_col=sql.func.abs(sql.column("value")).label("abs(value)")``, or ``index_col=cast(sql.column("id"),types.BigInteger).label("id")`` to convert the textfield ``id`` to ``BigInteger``. Note ``sql``, ``cast``, ``types`` methods comes from ``sqlalchemy`` module. Labeling columns created by functions or arithmetic operations is required. divisions: sequence Values of the index column to split the table by. If given, this will override npartitions and bytes_per_chunk. The divisions are the value boundaries of the index column used to define the partitions. For example, ``divisions=list('acegikmoqsuwz')`` could be used to partition a string column lexographically into 12 partitions, with the implicit assumption that each partition contains similar numbers of records. npartitions : int Number of partitions, if divisions is not given. Will split the values of the index column linearly between limits, if given, or the column max/min. The index column must be numeric or time for this to work limits: 2-tuple or None Manually give upper and lower range of values for use with npartitions; if None, first fetches max/min from the DB. Upper limit, if given, is inclusive. columns : list of strings or None Which columns to select; if None, gets all; can include sqlalchemy functions, e.g., ``sql.func.abs(sql.column('value')).label('abs(value)')``. Labeling columns created by functions or arithmetic operations is recommended. bytes_per_chunk : str, int If both divisions and npartitions is None, this is the target size of each partition, in bytes head_rows : int How many rows to load for inferring the data-types, unless passing meta meta : empty DataFrame or None If provided, do not attempt to infer dtypes, but use these, coercing all chunks on load schema : str or None If using a table name, pass this to sqlalchemy to select which DB schema to use within the URI connection engine_kwargs : dict or None Specific db engine parameters for sqlalchemy kwargs : dict Additional parameters to pass to `pd.read_sql()` Returns ------- dask.dataframe Examples -------- >>> df = dd.read_sql_table('accounts', 'sqlite:///path/to/bank.db', ... npartitions=10, index_col='id') # doctest: +SKIP """ import sqlalchemy as sa from sqlalchemy import sql from sqlalchemy.sql import elements if index_col is None: raise ValueError("Must specify index column to partition on") engine_kwargs = {} if engine_kwargs is None else engine_kwargs engine = sa.create_engine(uri, **engine_kwargs) m = sa.MetaData() if isinstance(table, str): table = sa.Table(table, m, autoload=True, autoload_with=engine, schema=schema) index = table.columns[index_col] if isinstance(index_col, str) else index_col if not isinstance(index_col, (str, elements.Label)): raise ValueError( "Use label when passing an SQLAlchemy instance as the index (%s)" % index ) if divisions and npartitions: raise TypeError("Must supply either divisions or npartitions, not both") columns = ( [(table.columns[c] if isinstance(c, str) else c) for c in columns] if columns else list(table.columns) ) if index not in columns: columns.append(index) if isinstance(index_col, str): kwargs["index_col"] = index_col else: # function names get pandas auto-named kwargs["index_col"] = index_col.name if head_rows > 0: # derive metadata from first few rows q = sql.select(columns).limit(head_rows).select_from(table) head = pd.read_sql(q, engine, **kwargs) if len(head) == 0: # no results at all name = table.name schema = table.schema head = pd.read_sql_table(name, uri, schema=schema, index_col=index_col) return from_pandas(head, npartitions=1) bytes_per_row = (head.memory_usage(deep=True, index=True)).sum() / head_rows if meta is None: meta = head.iloc[:0] elif meta is None: raise ValueError("Must provide meta if head_rows is 0") else: if divisions is None and npartitions is None: raise ValueError( "Must provide divisions or npartitions when using explicit meta." ) if divisions is None: if limits is None: # calculate max and min for given index q = sql.select([sql.func.max(index), sql.func.min(index)]).select_from( table ) minmax = pd.read_sql(q, engine) maxi, mini = minmax.iloc[0] dtype = minmax.dtypes["max_1"] else: mini, maxi = limits dtype = pd.Series(limits).dtype if npartitions is None: q = sql.select([sql.func.count(index)]).select_from(table) count = pd.read_sql(q, engine)["count_1"][0] npartitions = ( int( round( count * bytes_per_row / dask.utils.parse_bytes(bytes_per_chunk) ) ) or 1 ) if dtype.kind == "M": divisions = methods.tolist( pd.date_range( start=mini, end=maxi, freq="%iS" % ((maxi - mini).total_seconds() / npartitions), ) ) divisions[0] = mini divisions[-1] = maxi elif dtype.kind in ["i", "u", "f"]: divisions = np.linspace(mini, maxi, npartitions + 1).tolist() else: raise TypeError( 'Provided index column is of type "{}". If divisions is not provided the ' "index column type must be numeric or datetime.".format(dtype) ) parts = [] lowers, uppers = divisions[:-1], divisions[1:] for i, (lower, upper) in enumerate(zip(lowers, uppers)): cond = index <= upper if i == len(lowers) - 1 else index < upper q = sql.select(columns).where(sql.and_(index >= lower, cond)).select_from(table) parts.append( delayed(_read_sql_chunk)( q, uri, meta, engine_kwargs=engine_kwargs, **kwargs ) ) engine.dispose() return from_delayed(parts, meta, divisions=divisions)
def _read_sql_chunk(q, uri, meta, engine_kwargs=None, **kwargs): import sqlalchemy as sa engine_kwargs = engine_kwargs or {} engine = sa.create_engine(uri, **engine_kwargs) df = pd.read_sql(q, engine, **kwargs) engine.dispose() if len(df) == 0: return meta elif len(meta.dtypes.to_dict()) == 0: # only index column in loaded # required only for pandas < 1.0.0 return df else: return df.astype(meta.dtypes.to_dict(), copy=False)
[docs]def to_sql( df, name: str, uri: str, schema=None, if_exists: str = "fail", index: bool = True, index_label=None, chunksize=None, dtype=None, method=None, compute=True, parallel=False, ): """Store Dask Dataframe to a SQL table An empty table is created based on the "meta" DataFrame (and conforming to the caller's "if_exists" preference), and then each block calls pd.DataFrame.to_sql (with `if_exists="append"`). Databases supported by SQLAlchemy [1]_ are supported. Tables can be newly created, appended to, or overwritten. Parameters ---------- name : str Name of SQL table. uri : string Full sqlalchemy URI for the database connection schema : str, optional Specify the schema (if database flavor supports this). If None, use default schema. if_exists : {'fail', 'replace', 'append'}, default 'fail' How to behave if the table already exists. * fail: Raise a ValueError. * replace: Drop the table before inserting new values. * append: Insert new values to the existing table. index : bool, default True Write DataFrame index as a column. Uses `index_label` as the column name in the table. index_label : str or sequence, default None Column label for index column(s). If None is given (default) and `index` is True, then the index names are used. A sequence should be given if the DataFrame uses MultiIndex. chunksize : int, optional Specify the number of rows in each batch to be written at a time. By default, all rows will be written at once. dtype : dict or scalar, optional Specifying the datatype for columns. If a dictionary is used, the keys should be the column names and the values should be the SQLAlchemy types or strings for the sqlite3 legacy mode. If a scalar is provided, it will be applied to all columns. method : {None, 'multi', callable}, optional Controls the SQL insertion clause used: * None : Uses standard SQL ``INSERT`` clause (one per row). * 'multi': Pass multiple values in a single ``INSERT`` clause. * callable with signature ``(pd_table, conn, keys, data_iter)``. Details and a sample callable implementation can be found in the section :ref:`insert method <io.sql.method>`. compute : bool, default True When true, call dask.compute and perform the load into SQL; otherwise, return a Dask object (or array of per-block objects when parallel=True) parallel : bool, default False When true, have each block append itself to the DB table concurrently. This can result in DB rows being in a different order than the source DataFrame's corresponding rows. When false, load each block into the SQL DB in sequence. Raises ------ ValueError When the table already exists and `if_exists` is 'fail' (the default). See Also -------- read_sql : Read a DataFrame from a table. Notes ----- Timezone aware datetime columns will be written as ``Timestamp with timezone`` type with SQLAlchemy if supported by the database. Otherwise, the datetimes will be stored as timezone unaware timestamps local to the original timezone. .. versionadded:: 0.24.0 References ---------- .. [1] https://docs.sqlalchemy.org .. [2] https://www.python.org/dev/peps/pep-0249/ Examples -------- Create a table from scratch with 4 rows. >>> import pandas as pd >>> df = pd.DataFrame([ {'i':i, 's':str(i)*2 } for i in range(4) ]) >>> from dask.dataframe import from_pandas >>> ddf = from_pandas(df, npartitions=2) >>> ddf # doctest: +SKIP Dask DataFrame Structure: i s npartitions=2 0 int64 object 2 ... ... 3 ... ... Dask Name: from_pandas, 2 tasks >>> from dask.utils import tmpfile >>> from sqlalchemy import create_engine >>> with tmpfile() as f: ... db = 'sqlite:///%s' %f ... ddf.to_sql('test', db) ... engine = create_engine(db, echo=False) ... result = engine.execute("SELECT * FROM test").fetchall() >>> result [(0, 0, '00'), (1, 1, '11'), (2, 2, '22'), (3, 3, '33')] """ if not isinstance(uri, str): raise ValueError(f"Expected URI to be a string, got {type(uri)}.") # This is the only argument we add on top of what Pandas supports kwargs = dict( name=name, con=uri, schema=schema, if_exists=if_exists, index=index, index_label=index_label, chunksize=chunksize, dtype=dtype, method=method, ) def make_meta(meta): return meta.to_sql(**kwargs) make_meta = delayed(make_meta) meta_task = make_meta(df._meta) # Partitions should always append to the empty table created from `meta` above worker_kwargs = dict(kwargs, if_exists="append") if parallel: # Perform the meta insert, then one task that inserts all blocks concurrently: result = [ _extra_deps( d.to_sql, extras=meta_task, **worker_kwargs, dask_key_name="to_sql-%s" % tokenize(d, **worker_kwargs), ) for d in df.to_delayed() ] else: # Chain the "meta" insert and each block's insert result = [] last = meta_task for d in df.to_delayed(): result.append( _extra_deps( d.to_sql, extras=last, **worker_kwargs, dask_key_name="to_sql-%s" % tokenize(d, **worker_kwargs), ) ) last = result[-1] result = dask.delayed(result) if compute: dask.compute(result) else: return result
@delayed def _extra_deps(func, *args, extras=None, **kwargs): return func(*args, **kwargs)