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io.py
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import contextlib
import csv
import locale
import pickle
import re
import sys
import warnings
from typing import List, Iterable
from functools import lru_cache
from importlib import import_module
from itertools import chain
from os import path, remove
from tempfile import NamedTemporaryFile
from urllib.parse import urlparse, urlsplit, urlunsplit, \
unquote as urlunquote, quote
from urllib.request import urlopen, Request
from pathlib import Path
import numpy as np
import xlrd
import xlsxwriter
import openpyxl
from Orange.data import _io, Table, Domain, ContinuousVariable
from Orange.data import Compression, open_compressed, detect_encoding, \
isnastr, guess_data_type, sanitize_variable
from Orange.data.io_base import FileFormatBase, Flags, DataTableMixin, PICKLE_PROTOCOL
from Orange.util import flatten
# Support values longer than 128K (i.e. text contents features)
csv.field_size_limit(100*1024*1024)
__all__ = ["Flags", "FileFormat"]
Compression = Compression
open_compressed = open_compressed
detect_encoding = detect_encoding
isnastr = isnastr
guess_data_type = guess_data_type
sanitize_variable = sanitize_variable
Flags = Flags
FileFormatMeta = type(FileFormatBase)
class FileFormat(FileFormatBase):
"""
Subclasses set the following attributes and override the following methods:
EXTENSIONS = ('.ext1', '.ext2', ...)
DESCRIPTION = 'human-readable file format description'
SUPPORT_COMPRESSED = False
SUPPORT_SPARSE_DATA = False
def read(self):
... # load headers, data, ...
return self.data_table(data, headers)
@classmethod
def write_file(cls, filename, data):
...
self.write_headers(writer.write, data)
writer.writerows(data)
Wrapper FileFormat.data_table() returns Orange.data.Table from `data`
iterable (list (rows) of lists of values (cols)).
"""
# Priority when multiple formats support the same extension. Also
# the sort order in file open/save combo boxes. Lower is better.
PRIORITY = 10000
OPTIONAL_TYPE_ANNOTATIONS = False
SUPPORT_COMPRESSED = False
SUPPORT_SPARSE_DATA = False
def __init__(self, filename):
"""
Parameters
----------
filename : str
name of the file to open
"""
self.filename = filename
self.sheet = None
@property
def sheets(self) -> List:
"""FileFormats with a notion of sheets should override this property
to return a list of sheet names in the file.
Returns
-------
a list of sheet names
"""
return []
def select_sheet(self, sheet):
"""Select sheet to be read
Parameters
----------
sheet : str
sheet name
"""
self.sheet = sheet
def class_from_qualified_name(format_name):
""" File format class from qualified name. """
elements = format_name.split(".")
m = import_module(".".join(elements[:-1]))
return getattr(m, elements[-1])
class CSVReader(FileFormat, DataTableMixin):
"""Reader for comma separated files"""
EXTENSIONS = ('.csv',)
DESCRIPTION = 'Comma-separated values'
DELIMITERS = ',;:\t$ '
SUPPORT_COMPRESSED = True
SUPPORT_SPARSE_DATA = False
PRIORITY = 20
OPTIONAL_TYPE_ANNOTATIONS = True
def read(self):
for encoding in (lambda: ('us-ascii', None), # fast
lambda: (detect_encoding(self.filename), None), # precise
lambda: (locale.getpreferredencoding(False), None),
lambda: (sys.getdefaultencoding(), None), # desperate
lambda: ('utf-8', None), # ...
lambda: ('utf-8', 'ignore')): # fallback
encoding, errors = encoding()
# Clear the error flag for all except the last check, because
# the error of second-to-last check is stored and shown as warning in owfile
if errors != 'ignore':
error = ''
with self.open(self.filename, mode='rt', newline='',
encoding=encoding, errors=errors) as file:
# Sniff the CSV dialect (delimiter, quotes, ...)
try:
dialect = csv.Sniffer().sniff(
# Take first couple of *complete* lines as sample
''.join(file.readline() for _ in range(10)),
self.DELIMITERS)
delimiter = dialect.delimiter
quotechar = dialect.quotechar
except UnicodeDecodeError as e:
error = e
continue
except csv.Error:
delimiter = self.DELIMITERS[0]
quotechar = csv.excel.quotechar
file.seek(0)
try:
reader = csv.reader(
file, delimiter=delimiter, quotechar=quotechar,
skipinitialspace=True,
)
data = self.data_table(reader)
# TODO: Name can be set unconditionally when/if
# self.filename will always be a string with the file name.
# Currently, some tests pass StringIO instead of
# the file name to a reader.
if isinstance(self.filename, str):
data.name = path.splitext(
path.split(self.filename)[-1])[0]
if error and isinstance(error, UnicodeDecodeError):
pos, endpos = error.args[2], error.args[3]
warning = ('Skipped invalid byte(s) in position '
'{}{}').format(pos,
('-' + str(endpos)) if (endpos - pos) > 1 else '')
warnings.warn(warning)
self.set_table_metadata(self.filename, data)
return data
except Exception as e:
error = e
continue
raise ValueError('Cannot parse dataset {}: {}'.format(self.filename, error)) from error
@classmethod
def write_file(cls, filename, data, with_annotations=True):
with cls.open(filename, mode='wt', newline='', encoding='utf-8') as file:
writer = csv.writer(file, delimiter=cls.DELIMITERS[0])
cls.write_headers(writer.writerow, data, with_annotations)
cls.write_data(writer.writerow, data)
cls.write_table_metadata(filename, data)
class TabReader(CSVReader):
"""Reader for tab separated files"""
EXTENSIONS = ('.tab', '.tsv')
DESCRIPTION = 'Tab-separated values'
DELIMITERS = '\t'
PRIORITY = 10
class PickleReader(FileFormat):
"""Reader for pickled Table objects"""
EXTENSIONS = ('.pkl', '.pickle')
DESCRIPTION = 'Pickled Orange data'
SUPPORT_COMPRESSED = True
SUPPORT_SPARSE_DATA = True
def read(self):
with self.open(self.filename, 'rb') as f:
table = pickle.load(f)
if not isinstance(table, Table):
raise TypeError("file does not contain a data table")
else:
return table
@classmethod
def write_file(cls, filename, data):
with cls.open(filename, 'wb') as f:
pickle.dump(data, f, protocol=PICKLE_PROTOCOL)
class BasketReader(FileFormat):
"""Reader for basket (sparse) files"""
EXTENSIONS = ('.basket', '.bsk')
DESCRIPTION = 'Basket file'
SUPPORT_SPARSE_DATA = True
def read(self):
def constr_vars(inds):
if inds:
return [ContinuousVariable(x.decode("utf-8")) for _, x in
sorted((ind, name) for name, ind in inds.items())]
X, Y, metas, attr_indices, class_indices, meta_indices = \
_io.sparse_read_float(self.filename.encode(sys.getdefaultencoding()))
attrs = constr_vars(attr_indices)
classes = constr_vars(class_indices)
meta_attrs = constr_vars(meta_indices)
domain = Domain(attrs, classes, meta_attrs)
table = Table.from_numpy(
domain, attrs and X, classes and Y, metas and meta_attrs)
table.name = path.splitext(path.split(self.filename)[-1])[0]
return table
class _BaseExcelReader(FileFormat, DataTableMixin):
"""Base class for reading excel files"""
SUPPORT_COMPRESSED = False
SUPPORT_SPARSE_DATA = False
def __init__(self, filename):
super().__init__(filename=filename)
self._workbook = None
def get_cells(self) -> Iterable:
raise NotImplementedError
def read(self):
try:
cells = self.get_cells()
table = self.data_table(cells)
table.name = path.splitext(path.split(self.filename)[-1])[0]
if self.sheet and len(self.sheets) > 1:
table.name = '-'.join((table.name, self.sheet))
except Exception:
raise IOError("Couldn't load spreadsheet from " + self.filename)
return table
class ExcelReader(_BaseExcelReader):
"""Reader for .xlsx files"""
EXTENSIONS = ('.xlsx',)
DESCRIPTION = 'Microsoft Excel spreadsheet'
ERRORS = ("#VALUE!", "#DIV/0!", "#REF!", "#NUM!", "#NULL!", "#NAME?")
def __init__(self, filename):
super().__init__(filename)
self.sheet = self.workbook.active.title
@property
def workbook(self) -> openpyxl.Workbook:
if not self._workbook:
with warnings.catch_warnings():
# We don't care about extensions, but we hate warnings
warnings.filterwarnings(
"ignore",
".*extension is not supported and will be removed.*",
UserWarning)
self._workbook = openpyxl.load_workbook(self.filename,
data_only=True)
return self._workbook
@property
@lru_cache(1)
def sheets(self) -> List:
return self.workbook.sheetnames if self.workbook else []
def get_cells(self) -> Iterable:
def str_(x):
return str(x) if x is not None and x not in ExcelReader.ERRORS \
else ""
sheet = self._get_active_sheet()
min_col = sheet.min_column
max_col = sheet.max_column
cells = ([str_(cell.value) for cell in row[min_col - 1: max_col]]
for row in sheet.iter_rows(sheet.min_row, sheet.max_row + 1))
return filter(any, cells)
def _get_active_sheet(self) -> openpyxl.worksheet.worksheet.Worksheet:
if self.sheet:
return self.workbook[self.sheet]
else:
return self.workbook.active
@classmethod
def write_file(cls, filename, data):
vars = list(chain((ContinuousVariable('_w'),) if data.has_weights() else (),
data.domain.attributes,
data.domain.class_vars,
data.domain.metas))
formatters = [cls.formatter(v) for v in vars]
zipped_list_data = zip(data.W if data.W.ndim > 1 else data.W[:, np.newaxis],
data.X,
data.Y if data.Y.ndim > 1 else data.Y[:, np.newaxis],
data.metas)
headers = cls.header_names(data)
workbook = xlsxwriter.Workbook(filename)
sheet = workbook.add_worksheet()
for c, header in enumerate(headers):
sheet.write(0, c, header)
for i, row in enumerate(zipped_list_data, 1):
for j, (fmt, v) in enumerate(zip(formatters, flatten(row))):
sheet.write(i, j, fmt(v))
workbook.close()
class XlsReader(_BaseExcelReader):
"""Reader for .xls files"""
EXTENSIONS = ('.xls',)
DESCRIPTION = 'Microsoft Excel 97-2004 spreadsheet'
def __init__(self, filename):
super().__init__(filename)
self.sheet = self.workbook.sheet_by_index(0).name
@property
def workbook(self) -> xlrd.Book:
if not self._workbook:
self._workbook = xlrd.open_workbook(self.filename, on_demand=True)
return self._workbook
@property
@lru_cache(1)
def sheets(self) -> List:
return self.workbook.sheet_names() if self.workbook else []
def get_cells(self) -> Iterable:
def str_(cell):
return "" if cell.ctype == xlrd.XL_CELL_ERROR else str(cell.value)
sheet = self._get_active_sheet()
first_row = next(i for i in range(sheet.nrows)
if any(sheet.row_values(i)))
first_col = next(i for i in range(sheet.ncols)
if sheet.cell_value(first_row, i))
row_len = sheet.row_len(first_row)
return filter(any, ([str_(sheet.cell(row, col))
if col < sheet.row_len(row) else ''
for col in range(first_col, row_len)]
for row in range(first_row, sheet.nrows)))
def _get_active_sheet(self) -> xlrd.sheet.Sheet:
if self.sheet:
return self.workbook.sheet_by_name(self.sheet)
else:
return self.workbook.sheet_by_index(0)
class DotReader(FileFormat):
"""Writer for dot (graph) files"""
EXTENSIONS = ('.dot', '.gv')
DESCRIPTION = 'Dot graph description'
SUPPORT_COMPRESSED = True
SUPPORT_SPARSE_DATA = False
@classmethod
def write_graph(cls, filename, graph):
from sklearn import tree
tree.export_graphviz(graph, out_file=cls.open(filename, 'wt'))
@classmethod
def write(cls, filename, tree):
if type(tree) == dict:
tree = tree['tree']
cls.write_graph(filename, tree)
class UrlReader(FileFormat):
def __init__(self, filename):
filename = filename.strip()
if not urlparse(filename).scheme:
filename = 'http://' + filename
filename = quote(filename, safe="/:")
super().__init__(filename)
@staticmethod
def urlopen(url):
req = Request(
url,
# Avoid 403 error with servers that dislike scrapers
headers={'User-Agent': 'Mozilla/5.0 (X11; Linux) Gecko/20100101 Firefox/'})
return urlopen(req, timeout=10)
def read(self):
self.filename = self._trim(self._resolve_redirects(self.filename))
with contextlib.closing(self.urlopen(self.filename)) as response:
name = self._suggest_filename(response.headers['content-disposition'])
# using Path since splitext does not extract more extensions
extension = ''.join(Path(name).suffixes) # get only file extension
with NamedTemporaryFile(suffix=extension, delete=False) as f:
f.write(response.read())
# delete=False is a workaround for https://bugs.python.org/issue14243
reader = self.get_reader(f.name)
data = reader.read()
remove(f.name)
# Override name set in from_file() to avoid holding the temp prefix
data.name = path.splitext(name)[0]
data.origin = self.filename
return data
def _resolve_redirects(self, url):
# Resolve (potential) redirects to a final URL
with contextlib.closing(self.urlopen(url)) as response:
return response.url
@classmethod
def _trim(cls, url):
URL_TRIMMERS = (
cls._trim_googlesheet,
cls._trim_dropbox,
)
for trim in URL_TRIMMERS:
try:
url = trim(url)
except ValueError:
continue
else:
break
return url
@staticmethod
def _trim_googlesheet(url):
match = re.match(r'(?:https?://)?(?:www\.)?'
r'docs\.google\.com/spreadsheets/d/'
r'(?P<workbook_id>[-\w_]+)'
r'(?:/.*?gid=(?P<sheet_id>\d+).*|.*)?',
url, re.IGNORECASE)
try:
workbook, sheet = match.group('workbook_id'), match.group('sheet_id')
if not workbook:
raise ValueError
except (AttributeError, ValueError):
raise ValueError
url = 'https://docs.google.com/spreadsheets/d/{}/export?format=tsv'.format(workbook)
if sheet:
url += '&gid=' + sheet
return url
@staticmethod
def _trim_dropbox(url):
parts = urlsplit(url)
if not parts.netloc.endswith('dropbox.com'):
raise ValueError
return urlunsplit(parts._replace(query='dl=1'))
def _suggest_filename(self, content_disposition):
default_name = re.sub(r'[\\:/]', '_', urlparse(self.filename).path)
# See https://tools.ietf.org/html/rfc6266#section-4.1
matches = re.findall(r"filename\*?=(?:\"|.{0,10}?'[^']*')([^\"]+)",
content_disposition or '')
return urlunquote(matches[-1]) if matches else default_name