import base64 import contextlib import csv import enum import hashlib import io import itertools import json import os import sys from typing import Dict, cast, BinaryIO, Iterable, Iterator, Optional, Tuple, Type import click from . import recipes try: import pysqlite3 as sqlite3 # noqa: F401 from pysqlite3 import dbapi2 # noqa: F401 OperationalError = dbapi2.OperationalError except ImportError: try: import sqlean as sqlite3 # noqa: F401 from sqlean import dbapi2 # noqa: F401 OperationalError = dbapi2.OperationalError except ImportError: import sqlite3 # noqa: F401 from sqlite3 import dbapi2 # noqa: F401 OperationalError = dbapi2.OperationalError SPATIALITE_PATHS = ( "/usr/lib/x86_64-linux-gnu/mod_spatialite.so", "/usr/lib/aarch64-linux-gnu/mod_spatialite.so", "/usr/local/lib/mod_spatialite.dylib", "/usr/local/lib/mod_spatialite.so", "/opt/homebrew/lib/mod_spatialite.dylib", ) # Mainly so we can restore it if needed in the tests: ORIGINAL_CSV_FIELD_SIZE_LIMIT = csv.field_size_limit() class _CloseableIterator(Iterator[dict]): """Iterator wrapper that closes a file when iteration is complete.""" def __init__(self, iterator: Iterator[dict], closeable: io.IOBase): self._iterator = iterator self._closeable = closeable def __iter__(self) -> "_CloseableIterator": return self def __next__(self) -> dict: try: return next(self._iterator) except StopIteration: self._closeable.close() raise def close(self) -> None: self._closeable.close() 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 `__ 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) rows = _extra_key_strategy(reader, ignore_extras, extras_key) return _CloseableIterator(iter(rows), decoded_fp), 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) try: first_bytes = buffered.peek(2048).strip() except AttributeError: # Likely the user passed a TextIO when this needs a BytesIO raise TypeError( "rows_from_file() requires a file-like object that supports peek(), such as io.BytesIO" ) 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) -> str: 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} # Handle imports first so they're available for all approaches for import_ in imports: globals[import_.split(".")[0]] = __import__(import_) # If user defined a convert() function, return that try: exec(code, globals) return globals["convert"] except (AttributeError, SyntaxError, NameError, KeyError, TypeError): pass # Check if code is a direct callable reference # e.g. "r.parsedate" instead of "r.parsedate(value)" try: fn = eval(code, globals) if callable(fn): return fn except Exception: 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), "", "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") 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() def _flatten(d): for key, value in d.items(): if isinstance(value, dict): for key2, value2 in _flatten(value): yield key + "_" + key2, value2 else: yield key, value def flatten(row: dict) -> dict: """ Turn a nested dict e.g. ``{"a": {"b": 1}}`` into a flat dict: ``{"a_b": 1}`` :param row: A Python dictionary, optionally with nested dictionaries """ return dict(_flatten(row))