Merge pull request #359 from chezou/fallback-subprocess

feat: Fall back to subprocess if jpype fails

tabula/backend.py

@@ -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:/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:/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

tabula/io.py

@@ -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
@@ -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:/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,
@@ -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.
@@ -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.
 
@@ -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:
 
@@ -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)
@@ -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.
@@ -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.
 
@@ -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:
 
@@ -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)),
  )
 
@@ -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.
@@ -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.
 
@@ -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:
@@ -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)
@@ -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.
@@ -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.
 
@@ -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]: