feat: Use jpype instead of subprocess

pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
  "pandas >= 0.25.3",
  "numpy",
  "distro",
+ "jpype1",
 ]
 dynamic = ["version"]
 
@@ -75,3 +76,7 @@ exclude = [
 
 [tool.mypy]
 ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+# Disable faulthandler plugin on Windows to prevent spurious console noise
+addopts = "-p no:faulthandler"

tabula/io.py

@@ -23,17 +23,18 @@
 import os
 import platform
 import shlex
-import subprocess
 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 jpype
+import jpype.imports
 import numpy as np
 import pandas as pd
 
-from .errors import CSVParseError, JavaNotFoundError
+from .errors import CSVParseError
 from .file_util import localize_file
 from .template import load_template
 from .util import FileLikeObj, TabulaOption
@@ -55,51 +56,50 @@ def _jar_path() -> str:
  return os.environ.get("TABULA_JAR", DEFAULT_CONFIG["JAR_PATH"])
 
 
+def _call_tabula_java(options: TabulaOption, path: Optional[str] = None) -> str:
+ from java.lang import StringBuilder
+ from org.apache.commons.cli import DefaultParser
+ from technology import tabula
+
+ sb = StringBuilder()
+ parser = DefaultParser()
+
+ args = options.build_option_list()
+ if path:
+ args.insert(0, path)
+
+ cmd = parser.parse(tabula.CommandLineApp.buildOptions(), args)
+ tabula.CommandLineApp(sb, cmd).extractTables(cmd)
+ return str(sb.toString())
+
+
 def _run(
  java_options: List[str],
  options: TabulaOption,
  path: Optional[str] = None,
- encoding: str = "utf-8",
-) -> bytes:
+) -> 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 and an optional encoding to use for any required output sent to
- stderr.
-
- tabula-py options are translated into tabula-java options, see
- :func:`build_options` for more information.
+ argument to use for any required output sent to stderr.
  """
- # Workaround to enforce the silent option. See:
- # https:/tabulapdf/tabula-java/issues/231#issuecomment-397281157
- if options.silent:
- java_options.extend(
- (
- "-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
- "-Dorg.apache.commons.logging.Log"
- "=org.apache.commons.logging.impl.NoOpLog",
+
+ if not jpype.isJVMStarted():
+ jpype.addClassPath(_jar_path())
+
+ # Workaround to enforce the silent option. See:
+ # https:/tabulapdf/tabula-java/issues/231#issuecomment-397281157
+ if options.silent:
+ java_options.extend(
+ (
+ "-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
+ "-Dorg.apache.commons.logging.Log"
+ "=org.apache.commons.logging.impl.NoOpLog",
+ )
  )
- )
 
- args = ["java"] + java_options + ["-jar", _jar_path()] + options.build_option_list()
- if path:
- args.append(path)
+ jpype.startJVM(*java_options, convertStrings=False)
 
- 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(encoding)}")
- return result.stdout
- except FileNotFoundError:
- raise JavaNotFoundError(JAVA_NOT_FOUND_ERROR)
- except subprocess.CalledProcessError as e:
- logger.error(f"Error from tabula-java:\n{e.stderr.decode(encoding)}\n")
- raise
+ return _call_tabula_java(options, path)
 
 
 def read_pdf(
@@ -242,12 +242,6 @@ 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:
 
@@ -437,7 +431,7 @@ def read_pdf(
  _pandas_options = deepcopy(pandas_options)
  fmt = tabula_options.format
  if fmt == "JSON":
- raw_json: List[Any] = json.loads(output.decode(encoding))
+ raw_json: List[Any] = json.loads(output)
  if multiple_tables:
  return _extract_from(raw_json, _pandas_options)
  else:
@@ -447,7 +441,7 @@ def read_pdf(
  _pandas_options["encoding"] = _pandas_options.get("encoding", encoding)
 
  try:
- return [pd.read_csv(io.BytesIO(output), **_pandas_options)]
+ 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 += (
@@ -579,12 +573,6 @@ 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:
 
@@ -798,12 +786,6 @@ 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:
@@ -935,12 +917,6 @@ def convert_into_by_batch(
  Raises:
  ValueError:
  If input_dir doesn't exist.
-
- tabula.errors.JavaNotFoundError:
- If java is not installed or found.
-
- subprocess.CalledProcessError:
- If tabula-java execution failed.
  """
 
  if input_dir is None or not os.path.isdir(input_dir):

tests/test_read_pdf_jar_path.py

@@ -0,0 +1,20 @@
+import unittest
+from pathlib import Path
+from unittest.mock import patch
+
+import tabula
+
+
+class TestReadPdfJarPath(unittest.TestCase):
+ def setUp(self):
+ self.pdf_path = "tests/resources/data.pdf"
+
+ @patch("tabula.io._call_tabula_java")
+ @patch("tabula.io._jar_path")
+ def test_read_pdf_with_jar_path(self, jar_func, mock_fun):
+ jar_func.return_value = "/tmp/tabula-java.jar"
+
+ tabula.read_pdf(self.pdf_path, encoding="utf-8")
+ file_name = Path(tabula.io.jpype.getClassPath()).name
+ self.assertEqual(file_name, "tabula-java.jar")
+ mock_fun.assert_called_once()

tests/test_read_pdf_silent.py

@@ -0,0 +1,30 @@
+import platform
+import unittest
+from unittest.mock import patch
+
+import tabula
+
+
+class TestReadPdfJarPath(unittest.TestCase):
+ def setUp(self):
+ self.pdf_path = "tests/resources/data.pdf"
+
+ @patch("tabula.io._call_tabula_java")
+ @patch("tabula.io.jpype.startJVM")
+ def test_read_pdf_with_silent_true(self, jvm_func, mock_fun):
+ tabula.read_pdf(self.pdf_path, encoding="utf-8", silent=True)
+
+ target_args = []
+ if platform.system() == "Darwin":
+ target_args += ["-Djava.awt.headless=true"]
+ target_args += [
+ "-Dfile.encoding=UTF8",
+ "-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
+ "-Dorg.apache.commons.logging.Log=org.apache.commons.logging.impl.NoOpLog",
+ ]
+ jvm_func.assert_called_once_with(
+ *target_args,
+ convertStrings=False,
+ )
+
+ mock_fun.assert_called_once()

tests/test_read_pdf_table.py

@@ -1,13 +1,10 @@
 import filecmp
 import json
 import os
-import platform
 import shutil
-import subprocess
 import tempfile
 import unittest
 import uuid
-from unittest.mock import patch
 
 import pandas as pd # type: ignore
 
@@ -287,33 +284,6 @@ def test_read_pdf_with_binary_template(self):
  self.assertEqual(len(dfs), 4)
  self.assertTrue(dfs[0].equals(pd.read_csv(self.expected_csv1)))
 
- @patch("subprocess.run")
- @patch("tabula.io._jar_path")
- def test_read_pdf_with_jar_path(self, jar_func, mock_fun):
- jar_func.return_value = "/tmp/tabula-java.jar"
-
- tabula.read_pdf(self.pdf_path, encoding="utf-8")
-
- target_args = ["java"]
- if platform.system() == "Darwin":
- target_args += ["-Djava.awt.headless=true"]
- target_args += [
- "-Dfile.encoding=UTF8",
- "-jar",
- "/tmp/tabula-java.jar",
- "--guess",
- "--format",
- "JSON",
- "tests/resources/data.pdf",
- ]
- subp_args = {
- "stdout": subprocess.PIPE,
- "stderr": subprocess.PIPE,
- "stdin": subprocess.DEVNULL,
- "check": True,
- }
- mock_fun.assert_called_with(target_args, **subp_args)
-
  def test_read_pdf_with_dtype_string(self):
  pdf_path = "tests/resources/data_dtype.pdf"
  expected_csv = "tests/resources/data_dtype_expected.csv"
@@ -361,63 +331,6 @@ def test_read_pdf_with_dtype_string(self):
  dfs_template[0].equals(pd.read_csv(template_expected_csv, **pandas_options))
  )
 
- @patch("subprocess.run")
- @patch("tabula.io._jar_path")
- def test_read_pdf_with_silent_false(self, jar_func, mock_fun):
- jar_func.return_value = "/tmp/tabula-java.jar"
-
- tabula.read_pdf(self.pdf_path, encoding="utf-8", silent=False)
-
- target_args = ["java"]
- if platform.system() == "Darwin":
- target_args += ["-Djava.awt.headless=true"]
- target_args += [
- "-Dfile.encoding=UTF8",
- "-jar",
- "/tmp/tabula-java.jar",
- "--guess",
- "--format",
- "JSON",
- "tests/resources/data.pdf",
- ]
- subp_args = {
- "stdout": subprocess.PIPE,
- "stderr": subprocess.PIPE,
- "stdin": subprocess.DEVNULL,
- "check": True,
- }
- mock_fun.assert_called_with(target_args, **subp_args)
-
- @patch("subprocess.run")
- @patch("tabula.io._jar_path")
- def test_read_pdf_with_silent_true(self, jar_func, mock_fun):
- jar_func.return_value = "/tmp/tabula-java.jar"
-
- tabula.read_pdf(self.pdf_path, encoding="utf-8", silent=True)
-
- target_args = ["java"]
- if platform.system() == "Darwin":
- target_args += ["-Djava.awt.headless=true"]
- target_args += [
- "-Dfile.encoding=UTF8",
- "-Dorg.slf4j.simpleLogger.defaultLogLevel=off",
- "-Dorg.apache.commons.logging.Log=org.apache.commons.logging.impl.NoOpLog",
- "-jar",
- "/tmp/tabula-java.jar",
- "--guess",
- "--format",
- "JSON",
- "--silent",
- "tests/resources/data.pdf",
- ]
- subp_args = {
- "stdout": subprocess.PIPE,
- "stderr": subprocess.PIPE,
- "stdin": subprocess.DEVNULL,
- "check": True,
- }
- mock_fun.assert_called_with(target_args, **subp_args)
-
 
 if __name__ == "__main__":
  unittest.main()