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io.py
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"""This module is a wrapper of tabula, which enables table extraction from a PDF.
This module extracts tables from a PDF into a pandas DataFrame via jpype.
Instead of importing this module, you can import public interfaces such as
:func:`read_pdf()`, :func:`read_pdf_with_template()`, :func:`convert_into()`,
:func:`convert_into_by_batch()` from `tabula` module directory.
Note:
If you want to use your own tabula-java JAR file, set ``TABULA_JAR`` to
environment variable for JAR path.
Example:
>>> import tabula
>>> dfs = tabula.read_pdf("/path/to/sample.pdf", pages="all")
"""
import errno
import io
import json
import os
import platform
import shlex
from collections import defaultdict
from copy import deepcopy
from dataclasses import asdict
from logging import getLogger
from typing import Any, Dict, Iterable, List, Optional, Tuple, Union
import numpy as np
import pandas as pd
from .backend import SubprocessTabula, TabulaVm
from .errors import CSVParseError
from .file_util import localize_file
from .template import load_template
from .util import FileLikeObj, TabulaOption
logger = getLogger(__name__)
_tabula_vm: Optional[Union[TabulaVm, SubprocessTabula]] = None
def _run(
java_options: List[str],
options: TabulaOption,
path: Optional[str] = None,
encoding: str = "utf-8",
force_subprocess: bool = False,
) -> str:
"""Call tabula-java with the given lists of Java options and tabula-py
options, as well as an optional path to pass to tabula-java as a regular
argument to use for any required output sent to stderr.
"""
# Ignore some options that are set by tabula-py
IGNORED_JAVA_OPTIONS = {
"-Djava.awt.headless=true",
"-Dfile.encoding=UTF8",
"-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
"-Dorg.apache.commons.logging.Log=org.apache.commons.logging.impl.NoOpLog",
}
global _tabula_vm
if force_subprocess:
_tabula_vm = SubprocessTabula(
java_options=java_options, silent=options.silent, encoding=encoding
)
if not _tabula_vm:
_tabula_vm = TabulaVm(java_options=java_options, silent=options.silent)
if _tabula_vm and not _tabula_vm.tabula:
_tabula_vm = SubprocessTabula(
java_options=java_options, silent=options.silent, encoding=encoding
)
elif set(java_options) - IGNORED_JAVA_OPTIONS:
logger.warning("java_options is ignored until rebooting the Python process.")
return _tabula_vm.call_tabula_java(options, path)
def read_pdf(
input_path: FileLikeObj,
output_format: Optional[str] = None,
encoding: str = "utf-8",
java_options: Optional[List[str]] = None,
pandas_options: Optional[Dict[str, Any]] = None,
multiple_tables: bool = True,
user_agent: Optional[str] = None,
use_raw_url: bool = False,
pages: Optional[Union[str, int, Iterable[int]]] = None,
guess: bool = True,
area: Optional[Union[Iterable[float], Iterable[Iterable[float]]]] = None,
relative_area: bool = False,
lattice: bool = False,
stream: bool = False,
password: Optional[str] = None,
silent: Optional[bool] = None,
columns: Optional[Iterable[float]] = None,
relative_columns: bool = False,
format: Optional[str] = None,
batch: Optional[str] = None,
output_path: Optional[str] = None,
force_subprocess: bool = False,
options: str = "",
) -> Union[List[pd.DataFrame], Dict[str, Any]]:
"""Read tables in PDF.
Args:
input_path (str, path object or file-like object):
File like object of target PDF file.
It can be URL, which is downloaded by tabula-py automatically.
output_format (str, optional):
Output format for returned object (``dataframe`` or ``json``)
Giving this option enforces to ignore `multiple_tables` option.
encoding (str, optional):
Encoding type for pandas. Default: ``utf-8``
java_options (list, optional):
Set java options. This option will be ignored once JVM is launched.
Example:
``["-Xmx256m"]``
pandas_options (dict, optional):
Set pandas options.
Example:
``{'header': None}``
Note:
With ``multiple_tables=True`` (default), pandas_options is passed
to pandas.DataFrame, otherwise it is passed to pandas.read_csv.
Those two functions are different for accept options like ``dtype``.
multiple_tables (bool):
It enables to handle multiple tables within a page. Default: ``True``
Note:
If `multiple_tables` option is enabled, tabula-py uses not
:func:`pd.read_csv()`, but :func:`pd.DataFrame()`. Make
sure to pass appropriate `pandas_options`.
user_agent (str, optional):
Set a custom user-agent when download a pdf from a url. Otherwise
it uses the default ``urllib.request`` user-agent.
use_raw_url (bool):
It enforces to use `input_path` string for url without quoting/dequoting.
Default: False
pages (str, int, `iterable` of `int`, optional):
An optional values specifying pages to extract from. It allows
`str`,`int`, `iterable` of :`int`. Default: `1`
Examples:
``'1-2,3'``, ``'all'``, ``[1,2]``
guess (bool, optional):
Guess the portion of the page to analyze per page. Default `True`
If you use "area" option, this option becomes `False`.
Note:
As of tabula-java 1.0.3, guess option becomes independent from
lattice and stream option, you can use guess and lattice/stream option
at the same time.
area (iterable of float, iterable of iterable of float, optional):
Portion of the page to analyze(top,left,bottom,right).
Default is entire page.
Note:
If you want to use multiple area options and extract in one table, it
should be better to set ``multiple_tables=False`` for :func:`read_pdf()`
Examples:
``[269.875,12.75,790.5,561]``,
``[[12.1,20.5,30.1,50.2], [1.0,3.2,10.5,40.2]]``
relative_area (bool, optional):
If all area values are between 0-100 (inclusive) and preceded by ``'%'``,
input will be taken as % of actual height or width of the page.
Default ``False``.
lattice (bool, optional):
Force PDF to be extracted using lattice-mode extraction
(if there are ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
stream (bool, optional):
Force PDF to be extracted using stream-mode extraction
(if there are no ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
password (str, optional):
Password to decrypt document. Default: empty
silent (bool, optional):
Suppress all stderr output.
columns (iterable, optional):
X coordinates of column boundaries.
Example:
``[10.1, 20.2, 30.3]``
relative_columns (bool, optional):
If all values are between 0-100 (inclusive) and preceded by '%',
input will be taken as % of actual width of the page.
Default ``False``.
format (str, optional):
Format for output file or extracted object.
(``"CSV"``, ``"TSV"``, ``"JSON"``)
batch (str, optional):
Convert all PDF files in the provided directory. This argument should be
directory path.
output_path (str, optional):
Output file path. File format of it is depends on ``format``.
Same as ``--outfile`` option of tabula-java.
force_subprocess (bool):
Force to use tabula-java subprocess mode. If you have some issue with
jpype, try this option with same environment.
Default ``False``.
options (str, optional):
Raw option string for tabula-java.
Returns:
list of DataFrames or dict.
Raises:
FileNotFoundError:
If downloaded remote file doesn't exist.
ValueError:
If output_format is unknown format, or if downloaded remote file size is 0.
tabula.errors.CSVParseError:
If pandas CSV parsing failed.
tabula.errors.JavaNotFoundError:
If java is not installed or found.
subprocess.CalledProcessError:
If tabula-java execution failed.
Examples:
Here is a simple example.
Note that :func:`read_pdf()` only extract page 1 by default.
Notes:
As of tabula-py 2.0.0, :func:`read_pdf()` sets `multiple_tables=True` by
default. If you want to get consistent output with previous version, set
`multiple_tables=False`.
>>> import tabula
>>> pdf_path = "https://github.com/chezou/tabula-py/raw/master/tests/resources/data.pdf"
>>> tabula.read_pdf(pdf_path, stream=True)
[ Unnamed: 0 mpg cyl disp hp drat wt qsec vs am gear carb
0 Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
1 Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
2 Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
3 Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
4 Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
5 Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
6 Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4
7 Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
8 Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
9 Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4
10 Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4
11 Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3
12 Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3
13 Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3
14 Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4
15 Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4
16 Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4
17 Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
18 Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
19 Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
20 Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1
21 Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2
22 AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2
23 Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4
24 Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2
25 Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
26 Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
27 Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2
28 Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4
29 Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6
30 Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8
31 Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2]
If you want to extract all pages, set ``pages="all"``.
>>> dfs = tabula.read_pdf(pdf_path, pages="all")
>>> len(dfs)
4
>>> dfs
[ 0 1 2 3 4 5 6 7 8 9
0 mpg cyl disp hp drat wt qsec vs am gear
1 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4
2 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4
3 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4
4 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3
5 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3
6 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3
7 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3
8 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4
9 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4
10 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4
11 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4
12 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3
13 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3
14 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3
15 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3
16 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3
17 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3
18 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4
19 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4
20 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4
21 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3
22 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3
23 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3
24 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3
25 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3
26 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4
27 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5
28 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5
29 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5
30 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5
31 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5, 0 1 2 3 4
0 Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa, 0 1 2 3 4 5
0 NaN Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 145 6.7 3.3 5.7 2.5 virginica
2 146 6.7 3.0 5.2 2.3 virginica
3 147 6.3 2.5 5.0 1.9 virginica
4 148 6.5 3.0 5.2 2.0 virginica
5 149 6.2 3.4 5.4 2.3 virginica
6 150 5.9 3.0 5.1 1.8 virginica, 0
0 supp
1 VC
2 VC
3 VC
4 VC
5 VC
6 VC
7 VC
8 VC
9 VC
10 VC
11 VC
12 VC
13 VC
14 VC]
""" # noqa
format = None
if output_format:
# Respects explicit output_format
multiple_tables = False
if output_format.lower() == "dataframe":
pass
elif output_format.lower() == "json":
format = "JSON"
else:
raise ValueError(f"Unknown {output_format=}")
if multiple_tables:
format = "JSON"
tabula_options = TabulaOption(
pages=pages,
guess=guess,
area=area,
relative_area=relative_area,
lattice=lattice,
stream=stream,
password=password,
silent=silent,
columns=columns,
relative_columns=relative_columns,
format=format,
batch=batch,
output_path=output_path,
options=options,
multiple_tables=multiple_tables,
)
if java_options is None:
java_options = []
elif isinstance(java_options, str):
java_options = shlex.split(java_options)
# to prevent tabula-py from stealing focus on every call on mac
if platform.system() == "Darwin":
if not any("java.awt.headless" in opt for opt in java_options):
java_options += ["-Djava.awt.headless=true"]
if encoding == "utf-8":
if not any("file.encoding" in opt for opt in java_options):
java_options += ["-Dfile.encoding=UTF8"]
path, temporary = localize_file(input_path, user_agent, use_raw_url=use_raw_url)
if not os.path.exists(path):
raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
if os.path.getsize(path) == 0:
raise ValueError(f"{path} is empty. Check the file, or download it manually.")
try:
output = _run(
java_options,
tabula_options,
path,
encoding=encoding,
force_subprocess=force_subprocess,
)
finally:
if temporary:
os.unlink(path)
if len(output) == 0:
logger.warning("The output file is empty.")
return []
if pandas_options is None:
pandas_options = {}
_pandas_options = deepcopy(pandas_options)
fmt = tabula_options.format
if fmt == "JSON":
raw_json: List[Any] = json.loads(output)
if multiple_tables:
return _extract_from(raw_json, _pandas_options)
else:
return raw_json
else:
_pandas_options["encoding"] = _pandas_options.get("encoding", encoding)
try:
return [pd.read_csv(io.StringIO(output), **_pandas_options)]
except pd.errors.ParserError as e:
message = "Error failed to create DataFrame with different column tables.\n"
message += (
"Try to set `multiple_tables=True`"
"or set `names` option for `pandas_options`. \n"
)
raise CSVParseError(message, e)
def read_pdf_with_template(
input_path: FileLikeObj,
template_path: FileLikeObj,
pandas_options: Optional[Dict[str, Any]] = None,
encoding: str = "utf-8",
java_options: Optional[List[str]] = None,
user_agent: Optional[str] = None,
use_raw_url: bool = False,
pages: Optional[Union[str, int, Iterable[int]]] = None,
guess: bool = False,
area: Optional[Union[Iterable[float], Iterable[Iterable[float]]]] = None,
relative_area: bool = False,
lattice: bool = False,
stream: bool = False,
password: Optional[str] = None,
silent: Optional[bool] = None,
columns: Optional[List[float]] = None,
relative_columns: bool = False,
format: Optional[str] = None,
batch: Optional[str] = None,
output_path: Optional[str] = None,
force_subprocess: bool = False,
options: Optional[str] = None,
) -> List[pd.DataFrame]:
"""Read tables in PDF with a Tabula App template.
Args:
input_path (str, path object or file-like object):
File like object of target PDF file.
It can be URL, which is downloaded by tabula-py automatically.
template_path (str, path object or file-like object):
File like object for Tabula app template.
It can be URL, which is downloaded by tabula-py automatically.
pandas_options (dict, optional):
Set pandas options like {'header': None}.
encoding (str, optional):
Encoding type for pandas. Default is 'utf-8'
java_options (list, optional):
Set java options like ``["-Xmx256m"]``.
This option will be ignored once JVM is launched.
user_agent (str, optional):
Set a custom user-agent when download a pdf from a url. Otherwise
it uses the default ``urllib.request`` user-agent.
use_raw_url (bool):
It enforces to use `input_path` string for url without quoting/dequoting.
Default: False
pages (str, int, `iterable` of `int`, optional):
An optional values specifying pages to extract from. It allows
`str`,`int`, `iterable` of :`int`. Default: `1`
Examples:
``'1-2,3'``, ``'all'``, ``[1,2]``
guess (bool, optional):
Guess the portion of the page to analyze per page. Default `True`
If you use "area" option, this option becomes `False`.
Note:
As of tabula-java 1.0.3, guess option becomes independent from
lattice and stream option, you can use guess and lattice/stream option
at the same time.
area (iterable of float, iterable of iterable of float, optional):
Portion of the page to analyze(top,left,bottom,right).
Default is entire page.
Note:
If you want to use multiple area options and extract in one table, it
should be better to set ``multiple_tables=False`` for :func:`read_pdf()`
Examples:
``[269.875,12.75,790.5,561]``,
``[[12.1,20.5,30.1,50.2], [1.0,3.2,10.5,40.2]]``
relative_area (bool, optional):
If all area values are between 0-100 (inclusive) and preceded by ``'%'``,
input will be taken as % of actual height or width of the page.
Default ``False``.
lattice (bool, optional):
Force PDF to be extracted using lattice-mode extraction
(if there are ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
stream (bool, optional):
Force PDF to be extracted using stream-mode extraction
(if there are no ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
password (str, optional):
Password to decrypt document. Default: empty
silent (bool, optional):
Suppress all stderr output.
columns (iterable, optional):
X coordinates of column boundaries.
Example:
``[10.1, 20.2, 30.3]``
relative_columns (bool, optional):
If all values are between 0-100 (inclusive) and preceded by '%',
input will be taken as % of actual width of the page.
Default ``False``.
format (str, optional):
Format for output file or extracted object.
(``"CSV"``, ``"TSV"``, ``"JSON"``)
batch (str, optional):
Convert all PDF files in the provided directory. This argument should be
directory path.
output_path (str, optional):
Output file path. File format of it is depends on ``format``.
Same as ``--outfile`` option of tabula-java.
force_subprocess (bool):
Force to use tabula-java subprocess mode. If you have some issue with
jpype, try this option with same environment.
Default ``False``.
options (str, optional):
Raw option string for tabula-java.
Returns:
list of DataFrame.
Raises:
FileNotFoundError:
If downloaded remote file doesn't exist.
ValueError:
If output_format is unknown format, or if downloaded remote file size is 0.
tabula.errors.CSVParseError:
If pandas CSV parsing failed.
tabula.errors.JavaNotFoundError:
If java is not installed or found.
subprocess.CalledProcessError:
If tabula-java execution failed.
Examples:
You can use template file extracted by tabula app.
>>> import tabula
>>> tabula.read_pdf_with_template(pdf_path, "/path/to/data.tabula-template.json")
[ Unnamed: 0 mpg cyl disp hp ... qsec vs am gear carb
0 Mazda RX4 21.0 6 160.0 110 ... 16.46 0 1 4 4
1 Mazda RX4 Wag 21.0 6 160.0 110 ... 17.02 0 1 4 4
2 Datsun 710 22.8 4 108.0 93 ... 18.61 1 1 4 1
3 Hornet 4 Drive 21.4 6 258.0 110 ... 19.44 1 0 3 1
4 Hornet Sportabout 18.7 8 360.0 175 ... 17.02 0 0 3 2
5 Valiant 18.1 6 225.0 105 ... 20.22 1 0 3 1
6 Duster 360 14.3 8 360.0 245 ... 15.84 0 0 3 4
7 Merc 240D 24.4 4 146.7 62 ... 20.00 1 0 4 2
8 Merc 230 22.8 4 140.8 95 ... 22.90 1 0 4 2
9 Merc 280 19.2 6 167.6 123 ... 18.30 1 0 4 4
10 Merc 280C 17.8 6 167.6 123 ... 18.90 1 0 4 4
11 Merc 450SE 16.4 8 275.8 180 ... 17.40 0 0 3 3
12 Merc 450SL 17.3 8 275.8 180 ... 17.60 0 0 3 3
13 Merc 450SLC 15.2 8 275.8 180 ... 18.00 0 0 3 3
14 Cadillac Fleetwood 10.4 8 472.0 205 ... 17.98 0 0 3 4
15 Lincoln Continental 10.4 8 460.0 215 ... 17.82 0 0 3 4
16 Chrysler Imperial 14.7 8 440.0 230 ... 17.42 0 0 3 4
17 Fiat 128 32.4 4 78.7 66 ... 19.47 1 1 4 1
18 Honda Civic 30.4 4 75.7 52 ... 18.52 1 1 4 2
19 Toyota Corolla 33.9 4 71.1 65 ... 19.90 1 1 4 1
20 Toyota Corona 21.5 4 120.1 97 ... 20.01 1 0 3 1
21 Dodge Challenger 15.5 8 318.0 150 ... 16.87 0 0 3 2
22 AMC Javelin 15.2 8 304.0 150 ... 17.30 0 0 3 2
23 Camaro Z28 13.3 8 350.0 245 ... 15.41 0 0 3 4
24 Pontiac Firebird 19.2 8 400.0 175 ... 17.05 0 0 3 2
25 Fiat X1-9 27.3 4 79.0 66 ... 18.90 1 1 4 1
26 Porsche 914-2 26.0 4 120.3 91 ... 16.70 0 1 5 2
27 Lotus Europa 30.4 4 95.1 113 ... 16.90 1 1 5 2
28 Ford Pantera L 15.8 8 351.0 264 ... 14.50 0 1 5 4
29 Ferrari Dino 19.7 6 145.0 175 ... 15.50 0 1 5 6
30 Maserati Bora 15.0 8 301.0 335 ... 14.60 0 1 5 8
31 Volvo 142E 21.4 4 121.0 109 ... 18.60 1 1 4 2
[32 rows x 12 columns],
0 1 2 3 4
0 NaN Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa,
0 1 2 3 4 5
0 NaN Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 145 6.7 3.3 5.7 2.5 virginica
2 146 6.7 3.0 5.2 2.3 virginica
3 147 6.3 2.5 5.0 1.9 virginica
4 148 6.5 3.0 5.2 2.0 virginica
5 149 6.2 3.4 5.4 2.3 virginica,
Unnamed: 0 supp dose
0 4.2 VC 0.5
1 11.5 VC 0.5
2 7.3 VC 0.5
3 5.8 VC 0.5
4 6.4 VC 0.5
5 10.0 VC 0.5
6 11.2 VC 0.5
7 11.2 VC 0.5
8 5.2 VC 0.5
9 7.0 VC 0.5
10 16.5 VC 1.0
11 16.5 VC 1.0
12 15.2 VC 1.0
13 17.3 VC 1.0]
""" # noqa
path, temporary = localize_file(
template_path, user_agent=user_agent, suffix=".json", use_raw_url=use_raw_url
)
_options = load_template(path)
_force_option = TabulaOption(
pages=pages,
guess=guess,
area=area,
relative_area=relative_area,
lattice=lattice,
stream=stream,
password=password,
silent=silent,
columns=columns,
relative_columns=relative_columns,
format=format,
batch=batch,
output_path=output_path,
options=options,
)
dataframes = []
try:
for option in _options:
_df = read_pdf(
input_path,
pandas_options=pandas_options,
encoding=encoding,
java_options=java_options,
force_subprocess=force_subprocess,
**asdict(_force_option.merge(option)),
)
if isinstance(_df, list):
dataframes.extend(_df)
else:
dataframes.append(_df)
finally:
if temporary:
os.unlink(path)
return dataframes
def convert_into(
input_path: FileLikeObj,
output_path: str,
output_format: str = "csv",
java_options: Optional[List[str]] = None,
pages: Optional[Union[str, int, Iterable[int]]] = None,
guess: bool = True,
area: Optional[Union[Iterable[float], Iterable[Iterable[float]]]] = None,
relative_area: bool = False,
lattice: bool = False,
stream: bool = False,
password: Optional[str] = None,
silent: Optional[bool] = None,
columns: Optional[Iterable[float]] = None,
relative_columns: bool = False,
format: Optional[str] = None,
batch: Optional[str] = None,
force_subprocess: bool = False,
options: str = "",
) -> None:
"""Convert tables from PDF into a file.
Output file will be saved into `output_path`.
Args:
input_path (file like obj):
File like object of target PDF file.
output_path (str):
File path of output file.
output_format (str, optional):
Output format of this function (``csv``, ``json`` or ``tsv``).
Default: ``csv``
java_options (list, optional):
Set java options. This option will be ignored once JVM is launched.
Example:
``"-Xmx256m"``.
pages (str, int, `iterable` of `int`, optional):
An optional values specifying pages to extract from. It allows
`str`,`int`, `iterable` of :`int`. Default: `1`
Examples:
``'1-2,3'``, ``'all'``, ``[1,2]``
guess (bool, optional):
Guess the portion of the page to analyze per page. Default `True`
If you use "area" option, this option becomes `False`.
Note:
As of tabula-java 1.0.3, guess option becomes independent from
lattice and stream option, you can use guess and lattice/stream option
at the same time.
area (iterable of float, iterable of iterable of float, optional):
Portion of the page to analyze(top,left,bottom,right).
Default is entire page.
Note:
If you want to use multiple area options and extract in one table, it
should be better to set ``multiple_tables=False`` for :func:`read_pdf()`
Examples:
``[269.875,12.75,790.5,561]``,
``[[12.1,20.5,30.1,50.2], [1.0,3.2,10.5,40.2]]``
relative_area (bool, optional):
If all area values are between 0-100 (inclusive) and preceded by ``'%'``,
input will be taken as % of actual height or width of the page.
Default ``False``.
lattice (bool, optional):
Force PDF to be extracted using lattice-mode extraction
(if there are ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
stream (bool, optional):
Force PDF to be extracted using stream-mode extraction
(if there are no ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
password (str, optional):
Password to decrypt document. Default: empty
silent (bool, optional):
Suppress all stderr output.
columns (iterable, optional):
X coordinates of column boundaries.
Example:
``[10.1, 20.2, 30.3]``
format (str, optional):
Format for output file or extracted object.
(``"CSV"``, ``"TSV"``, ``"JSON"``)
batch (str, optional):
Convert all PDF files in the provided directory. This argument should be
directory path.
force_subprocess (bool):
Force to use tabula-java subprocess mode. If you have some issue with
jpype, try this option with same environment.
Default ``False``.
options (str, optional):
Raw option string for tabula-java.
Raises:
FileNotFoundError:
If downloaded remote file doesn't exist.
ValueError:
If output_format is unknown format, or if downloaded remote file size is 0.
tabula.errors.JavaNotFoundError:
If java is not installed or found.
subprocess.CalledProcessError:
If tabula-java execution failed.
"""
if output_path is None or len(output_path) == 0:
raise ValueError("'output_path' shoud not be None or empty")
format = _extract_format_for_conversion(output_format)
tabula_options = TabulaOption(
pages=pages,
guess=guess,
area=area,
relative_area=relative_area,
lattice=lattice,
stream=stream,
password=password,
silent=silent,
columns=columns,
relative_columns=relative_columns,
format=format,
batch=batch,
output_path=output_path,
options=options,
)
java_options = _build_java_options(java_options)
path, temporary = localize_file(input_path)
if not os.path.exists(path):
raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
if os.path.getsize(path) == 0:
raise ValueError(f"{path} is empty. Check the file, or download it manually.")
try:
_run(java_options, tabula_options, path, force_subprocess=force_subprocess)
finally:
if temporary:
os.unlink(path)
def convert_into_by_batch(
input_dir: str,
output_format: str = "csv",
java_options: Optional[List[str]] = None,
pages: Optional[Union[str, int, Iterable[int]]] = None,
guess: bool = True,
area: Optional[Union[Iterable[float], Iterable[Iterable[float]]]] = None,
relative_area: bool = False,
lattice: bool = False,
stream: bool = False,
password: Optional[str] = None,
silent: Optional[bool] = None,
columns: Optional[Iterable[float]] = None,
relative_columns: bool = False,
format: Optional[str] = None,
output_path: Optional[str] = None,
force_subprocess: bool = False,
options: str = "",
) -> None:
"""Convert tables from PDFs in a directory.
Args:
input_dir (str):
Directory path.
output_format (str, optional):
Output format of this function (csv, json or tsv)
java_options (list, optional):
Set java options like `-Xmx256m`.
This option will be ignored once JVM is launched.
pages (str, int, `iterable` of `int`, optional):
An optional values specifying pages to extract from. It allows
`str`,`int`, `iterable` of :`int`. Default: `1`
Examples:
``'1-2,3'``, ``'all'``, ``[1,2]``
guess (bool, optional):
Guess the portion of the page to analyze per page. Default `True`
If you use "area" option, this option becomes `False`.
Note:
As of tabula-java 1.0.3, guess option becomes independent from
lattice and stream option, you can use guess and lattice/stream option
at the same time.
area (iterable of float, iterable of iterable of float, optional):
Portion of the page to analyze(top,left,bottom,right).
Default is entire page.
Note:
If you want to use multiple area options and extract in one table, it
should be better to set ``multiple_tables=False`` for :func:`read_pdf()`
Examples:
``[269.875,12.75,790.5,561]``,
``[[12.1,20.5,30.1,50.2], [1.0,3.2,10.5,40.2]]``
relative_area (bool, optional):
If all area values are between 0-100 (inclusive) and preceded by ``'%'``,
input will be taken as % of actual height or width of the page.
Default ``False``.
lattice (bool, optional):
Force PDF to be extracted using lattice-mode extraction
(if there are ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
stream (bool, optional):
Force PDF to be extracted using stream-mode extraction
(if there are no ruling lines separating each cell, as in a PDF of an
Excel spreadsheet)
password (str, optional):
Password to decrypt document. Default: empty
silent (bool, optional):
Suppress all stderr output.
columns (iterable, optional):
X coordinates of column boundaries.
Example:
``[10.1, 20.2, 30.3]``
relative_columns (bool, optional):
If all values are between 0-100 (inclusive) and preceded by '%',
input will be taken as % of actual width of the page.
Default ``False``.
format (str, optional):
Format for output file or extracted object.
(``"CSV"``, ``"TSV"``, ``"JSON"``)
force_subprocess (bool):
Force to use tabula-java subprocess mode. If you have some issue with
jpype, try this option with same environment.
Default ``False``.
options (str, optional):
Raw option string for tabula-java.
Returns:
Nothing. Outputs are saved into the same directory with `input_dir`
Raises:
ValueError:
If input_dir doesn't exist.
"""
if input_dir is None or not os.path.isdir(input_dir):
raise ValueError("'input_dir' should be an existing directory path")
format = _extract_format_for_conversion(output_format)
java_options = _build_java_options(java_options)
tabula_options = TabulaOption(
pages=pages,
guess=guess,
area=area,
relative_area=relative_area,
lattice=lattice,
stream=stream,
password=password,
silent=silent,
columns=columns,
relative_columns=relative_columns,
format=format,
batch=input_dir,
output_path=output_path,
options=options,
)
_run(java_options, tabula_options, force_subprocess=force_subprocess)
def _build_java_options(_java_options: Optional[List[str]] = None) -> List[str]:
if _java_options is None:
_java_options = []
elif isinstance(_java_options, str):
_java_options = shlex.split(_java_options)
# to prevent tabula-py from stealing focus on every call on mac
if platform.system() == "Darwin":
r = "java.awt.headless"
if not any(filter(r.find, _java_options)): # type: ignore
_java_options = _java_options + ["-Djava.awt.headless=true"]
return _java_options
def _extract_format_for_conversion(output_format: str = "csv") -> str:
if output_format.lower() == "csv":
return "CSV"
elif output_format.lower() == "json":
return "JSON"
elif output_format.lower() == "tsv":
return "TSV"
else:
raise ValueError(f"Unknown {output_format=}")
def _extract_from(
raw_json: List[Any], pandas_options: Optional[Dict[str, Any]] = None