Source code for dask.dataframe.io.sql

import warnings

import numpy as np
import pandas as pd

from dask.base import compute as dask_compute
from dask.dataframe import methods
from dask.dataframe.io.io import from_delayed, from_pandas
from dask.delayed import delayed, tokenize
from dask.utils import parse_bytes


[docs]def read_sql_query( sql, con, index_col, divisions=None, npartitions=None, limits=None, bytes_per_chunk="256 MiB", head_rows=5, meta=None, engine_kwargs=None, **kwargs, ): """ Read SQL query into a DataFrame. 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 ---------- sql : SQLAlchemy Selectable SQL query to be executed. TextClause is not supported con : str Full sqlalchemy URI for the database connection index_col : str 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``; otherwise must supply explicit ``divisions``. 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. bytes_per_chunk : str or 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, and memory per row meta : empty DataFrame or None If provided, do not attempt to infer dtypes, but use these, coercing all chunks on load engine_kwargs : dict or None Specific db engine parameters for sqlalchemy kwargs : dict Additional parameters to pass to `pd.read_sql()` Returns ------- dask.dataframe See Also -------- read_sql_table : Read SQL database table into a DataFrame. """ import sqlalchemy as sa if not isinstance(con, str): raise TypeError( "'con' must be of type str, not " + str(type(con)) + "Note: Dask does not support SQLAlchemy connectables here" ) if index_col is None: raise ValueError("Must specify index column to partition on") if not isinstance(index_col, (str, sa.Column, sa.sql.elements.ColumnClause)): raise ValueError( "'index_col' must be of type str or sa.Column, not " + str(type(index_col)) ) if not head_rows > 0: if meta is None: raise ValueError("Must provide 'meta' if 'head_rows' is 0") if divisions is None and npartitions is None: raise ValueError( "Must provide 'divisions' or 'npartitions' if 'head_rows' is 0" ) if divisions and npartitions: raise TypeError("Must supply either 'divisions' or 'npartitions', not both") engine_kwargs = {} if engine_kwargs is None else engine_kwargs engine = sa.create_engine(con, **engine_kwargs) index = ( sa.Column(index_col) if isinstance(index_col, str) else sa.Column(index_col.name, index_col.type) ) kwargs["index_col"] = index.name if head_rows > 0: # derive metadata from first few rows q = sql.limit(head_rows) head = pd.read_sql(q, engine, **kwargs) if len(head) == 0: # no results at all 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] if divisions is None: if limits is None: # calculate max and min for given index q = sa.sql.select( [sa.sql.func.max(index), sa.sql.func.min(index)] ).select_from(sql.subquery()) 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 = sa.sql.select([sa.sql.func.count(index)]).select_from(sql.subquery()) count = pd.read_sql(q, engine)["count_1"][0] npartitions = ( int(round(count * bytes_per_row / 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, dtype=dtype).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.where(sa.sql.and_(index >= lower, cond)) parts.append( delayed(_read_sql_chunk)( q, con, meta, engine_kwargs=engine_kwargs, **kwargs ) ) engine.dispose() return from_delayed(parts, meta, divisions=divisions)
[docs]def read_sql_table( table_name, con, 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, ): """ Read SQL database table into a DataFrame. 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_name : str Name of SQL table in database. con : str Full sqlalchemy URI for the database connection index_col : str 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``; otherwise must supply explicit ``divisions``. columns : sequence of str or SqlAlchemy column or None Which columns to select; if None, gets all. Note can be a mix of str and SqlAlchemy columns schema : str or None Pass this to sqlalchemy to select which DB schema to use within the URI connection 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. bytes_per_chunk : str or 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, and memory per row meta : empty DataFrame or None If provided, do not attempt to infer dtypes, but use these, coercing all chunks on load engine_kwargs : dict or None Specific db engine parameters for sqlalchemy kwargs : dict Additional parameters to pass to `pd.read_sql()` Returns ------- dask.dataframe See Also -------- read_sql_query : Read SQL query into a 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 if "table" in kwargs: warnings.warn( "The `table` keyword has been replaced by `table_name`. Please use `table_name` instead.", DeprecationWarning, ) table_name = kwargs.pop("table") if "uri" in kwargs: warnings.warn( "The `uri` keyword has been replaced by `con`. Please use `con` instead.", DeprecationWarning, ) con = kwargs.pop("uri") deprecated_args = False if not isinstance(table_name, str): warnings.warn( "`read_sql_table` will no longer support {}; please use a `table_name` of type str instead " "or use `read_sql_query`, if you are using a SQLAlchemy query".format( type(table_name) ), DeprecationWarning, ) deprecated_args = True if columns is not None: for col in columns: if not isinstance(col, (sa.Column, str)): warnings.warn( "`columns` will no longer support SQLAlchemy selectables; please use `read_sql_query` " "instead", DeprecationWarning, ) deprecated_args = True if not _gt14(): warnings.warn( "Dask will soon require SQLAlchemy 1.4 or newer. " "Please update your SQLAlchemy version. " "Friendly note: Upgrading to SQLAlchemy 1.4 may brake code. Do it with caution. ", category=DeprecationWarning, ) if deprecated_args or not _gt14(): return _old_read_sql_table( table=table_name, uri=con, index_col=index_col, divisions=divisions, npartitions=npartitions, limits=limits, columns=columns, bytes_per_chunk=bytes_per_chunk, head_rows=head_rows, schema=schema, meta=meta, engine_kwargs=engine_kwargs, **kwargs, ) if not isinstance(con, str): raise TypeError( "`con` must be of type str, not " + str(type(con)) + "Note: Dask does not support SQLAlchemy connectables here" ) engine_kwargs = {} if engine_kwargs is None else engine_kwargs engine = sa.create_engine(con, **engine_kwargs) m = sa.MetaData() if isinstance(table_name, str): table_name = sa.Table( table_name, m, autoload=True, autoload_with=engine, schema=schema ) else: raise TypeError( "`table_name` must be of type str, not " + str(type(table_name)) ) engine.dispose() columns = ( [ ( sa.Column(c, table_name.columns[c].type) if isinstance(c, str) else sa.Column(c.name, c.type) ) for c in columns ] if columns else [sa.Column(c.name, c.type) for c in table_name.columns] ) index = ( sa.Column(index_col, table_name.columns[index_col].type) if isinstance(index_col, str) else sa.Column(index_col.name, index_col.type) ) if index.name not in [c.name for c in columns]: columns.append(index) query = sql.select(columns).select_from(table_name) return read_sql_query( sql=query, con=con, index_col=index, divisions=divisions, npartitions=npartitions, limits=limits, bytes_per_chunk=bytes_per_chunk, head_rows=head_rows, meta=meta, engine_kwargs=engine_kwargs, **kwargs, )
[docs]def read_sql(sql, con, index_col, **kwargs): """ Read SQL query or database table into a DataFrame. This function is a convenience wrapper around ``read_sql_table`` and ``read_sql_query``. It will delegate to the specific function depending on the provided input. A SQL query will be routed to ``read_sql_query``, while a database table name will be routed to ``read_sql_table``. Note that the delegated function might have more specific notes about their functionality not listed here. Parameters ---------- sql : str or SQLAlchemy Selectable Name of SQL table in database or SQL query to be executed. TextClause is not supported con : str Full sqlalchemy URI for the database connection index_col : str 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``; otherwise must supply explicit ``divisions``. Returns ------- dask.dataframe See Also -------- read_sql_table : Read SQL database table into a DataFrame. read_sql_query : Read SQL query into a DataFrame. """ if isinstance(sql, str): return read_sql_table(sql, con, index_col, **kwargs) else: return read_sql_query(sql, con, index_col, **kwargs)
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) def _to_sql_chunk(d, uri, engine_kwargs=None, **kwargs): import sqlalchemy as sa engine_kwargs = engine_kwargs or {} engine = sa.create_engine(uri, **engine_kwargs) q = d.to_sql(con=engine, **kwargs) engine.dispose() return q def _gt14() -> bool: """ Check if sqlalchemy.__version__ is at least 1.4.0, when several deprecations were made. """ import sqlalchemy if ( sqlalchemy.__version__.startswith("0.") or sqlalchemy.__version__.startswith("1.0") or sqlalchemy.__version__.startswith("1.1") or sqlalchemy.__version__.startswith("1.2") or sqlalchemy.__version__.startswith("1.3") ): return False else: return True def _old_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 warnings.warn( "You are using a compatibility version of `read_sql_table` that will be " "removed in a future version of dask. This function existst to support " "old versions of SQLAlchemy (< 1.4). This compatibility function is less " "stable than the new version. We recommend you update your code.", DeprecationWarning, ) 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 / 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)
[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, engine_kwargs=None, ): """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. engine_kwargs : dict or None Specific db engine parameters for sqlalchemy 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 >>> import dask.dataframe as dd >>> df = pd.DataFrame([ {'i':i, 's':str(i)*2 } for i in range(4) ]) >>> ddf = dd.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, uri=uri, engine_kwargs=engine_kwargs, schema=schema, if_exists=if_exists, index=index, index_label=index_label, chunksize=chunksize, dtype=dtype, method=method, ) meta_task = delayed(_to_sql_chunk)(df._meta, **kwargs) # 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( _to_sql_chunk, d, 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( _to_sql_chunk, d, extras=last, **worker_kwargs, dask_key_name="to_sql-%s" % tokenize(d, **worker_kwargs), ) ) last = result[-1] result = delayed(result) if compute: dask_compute(result) else: return result
@delayed def _extra_deps(func, *args, extras=None, **kwargs): return func(*args, **kwargs)