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utils.py
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utils.py
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import base64
import contextlib
import csv
import enum
import hashlib
import io
import itertools
import json
import os
import sys
from . import recipes
from typing import Dict, cast, BinaryIO, Iterable, Optional, Tuple, Type
import click
try:
import pysqlite3 as sqlite3 # type: ignore
import pysqlite3.dbapi2 # type: ignore
OperationalError = pysqlite3.dbapi2.OperationalError
except ImportError:
# https://github.com/python/mypy/issues/1153#issuecomment-253842414
import sqlite3 # type: ignore
OperationalError = sqlite3.OperationalError
SPATIALITE_PATHS = (
"/usr/lib/x86_64-linux-gnu/mod_spatialite.so",
"/usr/local/lib/mod_spatialite.dylib",
)
# Mainly so we can restore it if needed in the tests:
ORIGINAL_CSV_FIELD_SIZE_LIMIT = csv.field_size_limit()
def maximize_csv_field_size_limit():
"""
Increase the CSV field size limit to the maximum possible.
"""
# https://stackoverflow.com/a/15063941
field_size_limit = sys.maxsize
while True:
try:
csv.field_size_limit(field_size_limit)
break
except OverflowError:
field_size_limit = int(field_size_limit / 10)
def find_spatialite() -> Optional[str]:
"""
The ``find_spatialite()`` function searches for the `SpatiaLite <https://www.gaia-gis.it/fossil/libspatialite/index>`__
SQLite extension in some common places. It returns a string path to the location, or ``None`` if SpatiaLite was not found.
You can use it in code like this:
.. code-block:: python
from sqlite_utils import Database
from sqlite_utils.utils import find_spatialite
db = Database("mydb.db")
spatialite = find_spatialite()
if spatialite:
db.conn.enable_load_extension(True)
db.conn.load_extension(spatialite)
# or use with db.init_spatialite like this
db.init_spatialite(find_spatialite())
"""
for path in SPATIALITE_PATHS:
if os.path.exists(path):
return path
return None
def suggest_column_types(records):
all_column_types = {}
for record in records:
for key, value in record.items():
all_column_types.setdefault(key, set()).add(type(value))
return types_for_column_types(all_column_types)
def types_for_column_types(all_column_types):
column_types = {}
for key, types in all_column_types.items():
# Ignore null values if at least one other type present:
if len(types) > 1:
types.discard(None.__class__)
if {None.__class__} == types:
t = str
elif len(types) == 1:
t = list(types)[0]
# But if it's a subclass of list / tuple / dict, use str
# instead as we will be storing it as JSON in the table
for superclass in (list, tuple, dict):
if issubclass(t, superclass):
t = str
elif {int, bool}.issuperset(types):
t = int
elif {int, float, bool}.issuperset(types):
t = float
elif {bytes, str}.issuperset(types):
t = bytes
else:
t = str
column_types[key] = t
return column_types
def column_affinity(column_type):
# Implementation of SQLite affinity rules from
# https://www.sqlite.org/datatype3.html#determination_of_column_affinity
assert isinstance(column_type, str)
column_type = column_type.upper().strip()
if column_type == "":
return str # We differ from spec, which says it should be BLOB
if "INT" in column_type:
return int
if "CHAR" in column_type or "CLOB" in column_type or "TEXT" in column_type:
return str
if "BLOB" in column_type:
return bytes
if "REAL" in column_type or "FLOA" in column_type or "DOUB" in column_type:
return float
# Default is 'NUMERIC', which we currently also treat as float
return float
def decode_base64_values(doc):
# Looks for '{"$base64": true..., "encoded": ...}' values and decodes them
to_fix = [
k
for k in doc
if isinstance(doc[k], dict)
and doc[k].get("$base64") is True
and "encoded" in doc[k]
]
if not to_fix:
return doc
return dict(doc, **{k: base64.b64decode(doc[k]["encoded"]) for k in to_fix})
class UpdateWrapper:
def __init__(self, wrapped, update):
self._wrapped = wrapped
self._update = update
def __iter__(self):
for line in self._wrapped:
self._update(len(line))
yield line
def read(self, size=-1):
data = self._wrapped.read(size)
self._update(len(data))
return data
@contextlib.contextmanager
def file_progress(file, silent=False, **kwargs):
if silent:
yield file
return
# file.fileno() throws an exception in our test suite
try:
fileno = file.fileno()
except io.UnsupportedOperation:
yield file
return
if fileno == 0: # 0 means stdin
yield file
else:
file_length = os.path.getsize(file.name)
with click.progressbar(length=file_length, **kwargs) as bar:
yield UpdateWrapper(file, bar.update)
class Format(enum.Enum):
CSV = 1
TSV = 2
JSON = 3
NL = 4
class RowsFromFileError(Exception):
pass
class RowsFromFileBadJSON(RowsFromFileError):
pass
class RowError(Exception):
pass
def _extra_key_strategy(
reader: Iterable[dict],
ignore_extras: Optional[bool] = False,
extras_key: Optional[str] = None,
) -> Iterable[dict]:
# Logic for handling CSV rows with more values than there are headings
for row in reader:
# DictReader adds a 'None' key with extra row values
if None not in row:
yield row
elif ignore_extras:
# ignoring row.pop(none) because of this issue:
# https://github.com/simonw/sqlite-utils/issues/440#issuecomment-1155358637
row.pop(None) # type: ignore
yield row
elif not extras_key:
extras = row.pop(None) # type: ignore
raise RowError(
"Row {} contained these extra values: {}".format(row, extras)
)
else:
row[extras_key] = row.pop(None) # type: ignore
yield row
def rows_from_file(
fp: BinaryIO,
format: Optional[Format] = None,
dialect: Optional[Type[csv.Dialect]] = None,
encoding: Optional[str] = None,
ignore_extras: Optional[bool] = False,
extras_key: Optional[str] = None,
) -> Tuple[Iterable[dict], Format]:
"""
Load a sequence of dictionaries from a file-like object containing one of four different formats.
.. code-block:: python
from sqlite_utils.utils import rows_from_file
import io
rows, format = rows_from_file(io.StringIO("id,name\\n1,Cleo")))
print(list(rows), format)
# Outputs [{'id': '1', 'name': 'Cleo'}] Format.CSV
This defaults to attempting to automatically detect the format of the data, or you can pass in an
explicit format using the format= option.
Returns a tuple of ``(rows_generator, format_used)`` where ``rows_generator`` can be iterated over
to return dictionaries, while ``format_used`` is a value from the ``sqlite_utils.utils.Format`` enum:
.. code-block:: python
class Format(enum.Enum):
CSV = 1
TSV = 2
JSON = 3
NL = 4
If a CSV or TSV file includes rows with more fields than are declared in the header a
``sqlite_utils.utils.RowError`` exception will be raised when you loop over the generator.
You can instead ignore the extra data by passing ``ignore_extras=True``.
Or pass ``extras_key="rest"`` to put those additional values in a list in a key called ``rest``.
:param fp: a file-like object containing binary data
:param format: the format to use - omit this to detect the format
:param dialect: the CSV dialect to use - omit this to detect the dialect
:param encoding: the character encoding to use when reading CSV/TSV data
:param ignore_extras: ignore any extra fields on rows
:param extras_key: put any extra fields in a list with this key
"""
if ignore_extras and extras_key:
raise ValueError("Cannot use ignore_extras= and extras_key= together")
if format == Format.JSON:
decoded = json.load(fp)
if isinstance(decoded, dict):
decoded = [decoded]
if not isinstance(decoded, list):
raise RowsFromFileBadJSON("JSON must be a list or a dictionary")
return decoded, Format.JSON
elif format == Format.NL:
return (json.loads(line) for line in fp if line.strip()), Format.NL
elif format == Format.CSV:
use_encoding: str = encoding or "utf-8-sig"
decoded_fp = io.TextIOWrapper(fp, encoding=use_encoding)
if dialect is not None:
reader = csv.DictReader(decoded_fp, dialect=dialect)
else:
reader = csv.DictReader(decoded_fp)
return _extra_key_strategy(reader, ignore_extras, extras_key), Format.CSV
elif format == Format.TSV:
rows = rows_from_file(
fp, format=Format.CSV, dialect=csv.excel_tab, encoding=encoding
)[0]
return (
_extra_key_strategy(rows, ignore_extras, extras_key),
Format.TSV,
)
elif format is None:
# Detect the format, then call this recursively
buffered = io.BufferedReader(cast(io.RawIOBase, fp), buffer_size=4096)
first_bytes = buffered.peek(2048).strip()
if first_bytes.startswith(b"[") or first_bytes.startswith(b"{"):
# TODO: Detect newline-JSON
return rows_from_file(buffered, format=Format.JSON)
else:
dialect = csv.Sniffer().sniff(
first_bytes.decode(encoding or "utf-8-sig", "ignore")
)
rows, _ = rows_from_file(
buffered, format=Format.CSV, dialect=dialect, encoding=encoding
)
# Make sure we return the format we detected
format = Format.TSV if dialect.delimiter == "\t" else Format.CSV
return _extra_key_strategy(rows, ignore_extras, extras_key), format
else:
raise RowsFromFileError("Bad format")
class TypeTracker:
"""
Wrap an iterator of dictionaries and keep track of which SQLite column
types are the most likely fit for each of their keys.
Example usage:
.. code-block:: python
from sqlite_utils.utils import TypeTracker
import sqlite_utils
db = sqlite_utils.Database(memory=True)
tracker = TypeTracker()
rows = [{"id": "1", "name": "Cleo", "id": "2", "name": "Cardi"}]
db["creatures"].insert_all(tracker.wrap(rows))
print(tracker.types)
# Outputs {'id': 'integer', 'name': 'text'}
db["creatures"].transform(types=tracker.types)
"""
def __init__(self):
self.trackers = {}
def wrap(self, iterator: Iterable[dict]) -> Iterable[dict]:
"""
Use this to loop through an existing iterator, tracking the column types
as part of the iteration.
:param iterator: The iterator to wrap
"""
for row in iterator:
for key, value in row.items():
tracker = self.trackers.setdefault(key, ValueTracker())
tracker.evaluate(value)
yield row
@property
def types(self) -> Dict[str, str]:
"""
A dictionary mapping column names to their detected types. This can be passed
to the ``db[table_name].transform(types=tracker.types)`` method.
"""
return {key: tracker.guessed_type for key, tracker in self.trackers.items()}
class ValueTracker:
def __init__(self):
self.couldbe = {key: getattr(self, "test_" + key) for key in self.get_tests()}
@classmethod
def get_tests(cls):
return [
key.split("test_")[-1]
for key in cls.__dict__.keys()
if key.startswith("test_")
]
def test_integer(self, value):
try:
int(value)
return True
except (ValueError, TypeError):
return False
def test_float(self, value):
try:
float(value)
return True
except (ValueError, TypeError):
return False
def __repr__(self):
return self.guessed_type + ": possibilities = " + repr(self.couldbe)
@property
def guessed_type(self):
options = set(self.couldbe.keys())
# Return based on precedence
for key in self.get_tests():
if key in options:
return key
return "text"
def evaluate(self, value):
if not value or not self.couldbe:
return
not_these = []
for name, test in self.couldbe.items():
if not test(value):
not_these.append(name)
for key in not_these:
del self.couldbe[key]
class NullProgressBar:
def __init__(self, *args):
self.args = args
def __iter__(self):
yield from self.args[0]
def update(self, value):
pass
@contextlib.contextmanager
def progressbar(*args, **kwargs):
silent = kwargs.pop("silent")
if silent:
yield NullProgressBar(*args)
else:
with click.progressbar(*args, **kwargs) as bar:
yield bar
def _compile_code(code, imports, variable="value"):
globals = {"r": recipes, "recipes": recipes}
# If user defined a convert() function, return that
try:
exec(code, globals)
return globals["convert"]
except (AttributeError, SyntaxError, NameError, KeyError, TypeError):
pass
# Try compiling their code as a function instead
body_variants = [code]
# If single line and no 'return', try adding the return
if "\n" not in code and not code.strip().startswith("return "):
body_variants.insert(0, "return {}".format(code))
code_o = None
for variant in body_variants:
new_code = ["def fn({}):".format(variable)]
for line in variant.split("\n"):
new_code.append(" {}".format(line))
try:
code_o = compile("\n".join(new_code), "<string>", "exec")
break
except SyntaxError:
# Try another variant, e.g. for 'return row["column"] = 1'
continue
if code_o is None:
raise SyntaxError("Could not compile code")
for import_ in imports:
globals[import_.split(".")[0]] = __import__(import_)
exec(code_o, globals)
return globals["fn"]
def chunks(sequence: Iterable, size: int) -> Iterable[Iterable]:
"""
Iterate over chunks of the sequence of the given size.
:param sequence: Any Python iterator
:param size: The size of each chunk
"""
iterator = iter(sequence)
for item in iterator:
yield itertools.chain([item], itertools.islice(iterator, size - 1))
def hash_record(record: Dict, keys: Optional[Iterable[str]] = None):
"""
``record`` should be a Python dictionary. Returns a sha1 hash of the
keys and values in that record.
If ``keys=`` is provided, uses just those keys to generate the hash.
Example usage::
from sqlite_utils.utils import hash_record
hashed = hash_record({"name": "Cleo", "twitter": "CleoPaws"})
# Or with the keys= option:
hashed = hash_record(
{"name": "Cleo", "twitter": "CleoPaws", "age": 7},
keys=("name", "twitter")
)
:param record: Record to generate a hash for
:param keys: Subset of keys to use for that hash
"""
to_hash = record
if keys is not None:
to_hash = {key: record[key] for key in keys}
return hashlib.sha1(
json.dumps(to_hash, separators=(",", ":"), sort_keys=True, default=repr).encode(
"utf8"
)
).hexdigest()