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
@@ -55,12 +56,29 @@ 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
@@ -69,37 +87,24 @@ def _run(
     tabula-py options are translated into tabula-java options, see
     :func:`build_options` for more information.
     """
-    # Workaround to enforce the silent option. See:
-    # https://github.com/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://github.com/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 +247,6 @@ 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 +436,7 @@ 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 +446,7 @@ 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 +578,6 @@ 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 +791,6 @@ 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 +922,6 @@ 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_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()