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Merge pull request #359 from chezou/fallback-subprocess
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feat: Fall back to subprocess if jpype fails
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@chezou
chezou authored Sep 22, 2023
2 parents 9bde1e5 + aca1abd commit dd9d111
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Showing 5 changed files with 196 additions and 67 deletions.
122 changes: 122 additions & 0 deletions tabula/backend.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,122 @@
import os
import subprocess
from logging import getLogger
from typing import List, Optional

import jpype
import jpype.imports

from .errors import JavaNotFoundError
from .util import TabulaOption

logger = getLogger(__name__)

JAVA_NOT_FOUND_ERROR = (
"`java` command is not found from this Python process."
"Please ensure Java is installed and PATH is set for `java`"
)
TABULA_JAVA_VERSION = "1.0.5"
JAR_NAME = f"tabula-{TABULA_JAVA_VERSION}-jar-with-dependencies.jar"
JAR_DIR = os.path.abspath(os.path.dirname(__file__))
DEFAULT_CONFIG = {"JAR_PATH": os.path.join(JAR_DIR, JAR_NAME)}


def jar_path() -> str:
return os.environ.get("TABULA_JAR", DEFAULT_CONFIG["JAR_PATH"])


class TabulaVm:
def __init__(self, java_options: List[str], silent: Optional[bool]) -> None:
if not jpype.isJVMStarted():
jpype.addClassPath(jar_path())

# Workaround to enforce the silent option. See:
# https://github.com/tabulapdf/tabula-java/issues/231#issuecomment-397281157
if silent:
java_options.extend(
(
"-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
"-Dorg.apache.commons.logging.Log"
"=org.apache.commons.logging.impl.NoOpLog",
)
)

jpype.startJVM(*java_options, convertStrings=False)

try:
import java.lang as lang
import technology.tabula as tabula
from org.apache.commons.cli import DefaultParser

self.tabula = tabula
self.parser = DefaultParser()
self.lang = lang
except (ModuleNotFoundError, ImportError) as e:
logger.warning(
"Error importing jpype dependencies. Fallback to subprocess."
)
logger.warning(jpype.java.lang.System.getProperty("java.class.path"))
logger.warning(e)
self.tabula = None
self.parse = None
self.lang = None

def call_tabula_java(
self, options: TabulaOption, path: Optional[str] = None
) -> str:
sb = self.lang.StringBuilder()
args = options.build_option_list()
if path:
args.insert(0, path)

cmd = self.parser.parse(self.tabula.CommandLineApp.buildOptions(), args)
self.tabula.CommandLineApp(sb, cmd).extractTables(cmd)
return str(sb.toString())


class SubprocessTabula:
def __init__(
self, java_options: List[str], silent: Optional[bool], encoding: str
) -> None:
# Workaround to enforce the silent option. See:
# https://github.com/tabulapdf/tabula-java/issues/231#issuecomment-397281157
if silent:
java_options.extend(
(
"-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
"-Dorg.apache.commons.logging.Log"
"=org.apache.commons.logging.impl.NoOpLog",
)
)

self.java_options = java_options
self.encoding = encoding

def call_tabula_java(
self, options: TabulaOption, path: Optional[str] = None
) -> str:
args = (
["java"]
+ self.java_options
+ ["-jar", jar_path()]
+ options.build_option_list()
)
if path:
args.append(path)

try:
result = subprocess.run(
args,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.DEVNULL,
check=True,
)
if result.stderr:
logger.warning(f"Got stderr: {result.stderr.decode(self.encoding)}")
return result.stdout.decode(self.encoding)
except FileNotFoundError:
raise JavaNotFoundError(JAVA_NOT_FOUND_ERROR)
except subprocess.CalledProcessError as e:
logger.error(f"Error from tabula-java:\n{e.stderr.decode(self.encoding)}\n")
raise
123 changes: 61 additions & 62 deletions tabula/io.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,36 +28,27 @@
from logging import getLogger
from typing import Any, Dict, Iterable, List, Optional, Tuple, Union

import jpype
import jpype.imports
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_JAVA_VERSION = "1.0.5"
JAR_NAME = f"tabula-{TABULA_JAVA_VERSION}-jar-with-dependencies.jar"
JAR_DIR = os.path.abspath(os.path.dirname(__file__))
JAVA_NOT_FOUND_ERROR = (
"`java` command is not found from this Python process."
"Please ensure Java is installed and PATH is set for `java`"
)

DEFAULT_CONFIG = {"JAR_PATH": os.path.join(JAR_DIR, JAR_NAME)}


_tabula_vm = None
_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
Expand All @@ -72,59 +63,23 @@ def _run(
}

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, options.silent)
_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)


class TabulaVm:
def __init__(self, java_options: List[str], silent: Optional[bool]) -> None:
if not jpype.isJVMStarted():
jpype.addClassPath(TabulaVm._jar_path())

# Workaround to enforce the silent option. See:
# https://github.com/tabulapdf/tabula-java/issues/231#issuecomment-397281157
if silent:
java_options.extend(
(
"-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
"-Dorg.apache.commons.logging.Log"
"=org.apache.commons.logging.impl.NoOpLog",
)
)

jpype.startJVM(*java_options, convertStrings=False)

from java import lang
from org.apache.commons import cli
from technology import tabula

self.tabula = tabula
self.cli = cli
self.lang = lang

@staticmethod
def _jar_path() -> str:
return os.environ.get("TABULA_JAR", DEFAULT_CONFIG["JAR_PATH"])

def call_tabula_java(
self, options: TabulaOption, path: Optional[str] = None
) -> str:
sb = self.lang.StringBuilder()
parser = self.cli.DefaultParser()

args = options.build_option_list()
if path:
args.insert(0, path)

cmd = parser.parse(self.tabula.CommandLineApp.buildOptions(), args)
self.tabula.CommandLineApp(sb, cmd).extractTables(cmd)
return str(sb.toString())


def read_pdf(
input_path: FileLikeObj,
output_format: Optional[str] = None,
Expand All @@ -147,6 +102,7 @@ def read_pdf(
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.
Expand Down Expand Up @@ -249,6 +205,10 @@ def read_pdf(
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.
Expand All @@ -265,6 +225,11 @@ def read_pdf(
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:
Expand Down Expand Up @@ -439,7 +404,13 @@ def read_pdf(
raise ValueError(f"{path} is empty. Check the file, or download it manually.")

try:
output = _run(java_options, tabula_options, path)
output = _run(
java_options,
tabula_options,
path,
encoding=encoding,
force_subprocess=force_subprocess,
)
finally:
if temporary:
os.unlink(path)
Expand Down Expand Up @@ -496,6 +467,7 @@ def read_pdf_with_template(
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.
Expand Down Expand Up @@ -581,6 +553,10 @@ def read_pdf_with_template(
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.
Expand All @@ -597,6 +573,12 @@ def read_pdf_with_template(
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:
Expand Down Expand Up @@ -698,6 +680,7 @@ def read_pdf_with_template(
pandas_options=pandas_options,
encoding=encoding,
java_options=java_options,
force_subprocess=force_subprocess,
**asdict(_force_option.merge(option)),
)

Expand Down Expand Up @@ -729,6 +712,7 @@ def convert_into(
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.
Expand Down Expand Up @@ -801,6 +785,10 @@ def convert_into(
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.
Expand All @@ -810,6 +798,12 @@ def convert_into(
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:
Expand Down Expand Up @@ -844,7 +838,7 @@ def convert_into(
raise ValueError(f"{path} is empty. Check the file, or download it manually.")

try:
_run(java_options, tabula_options, path)
_run(java_options, tabula_options, path, force_subprocess=force_subprocess)
finally:
if temporary:
os.unlink(path)
Expand All @@ -866,6 +860,7 @@ def convert_into_by_batch(
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.
Expand Down Expand Up @@ -933,6 +928,10 @@ def convert_into_by_batch(
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.
Expand Down Expand Up @@ -968,7 +967,7 @@ def convert_into_by_batch(
options=options,
)

_run(java_options, tabula_options)
_run(java_options, tabula_options, force_subprocess=force_subprocess)


def _build_java_options(_java_options: Optional[List[str]] = None) -> List[str]:
Expand Down
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