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609a08a95f
The table metrics considering spans is not used and it messes with the output thus I have cleaned the code from it. Though, I have left table_as_cells in the source code - it still may be useful for the users
437 lines
17 KiB
Python
437 lines
17 KiB
Python
import os
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import pathlib
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import shutil
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from pathlib import Path
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import numpy as np
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import pandas as pd
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import pytest
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from unstructured.metrics.evaluate import (
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ElementTypeMetricsCalculator,
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TableStructureMetricsCalculator,
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TextExtractionMetricsCalculator,
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filter_metrics,
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get_mean_grouping,
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)
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is_in_docker = os.path.exists("/.dockerenv")
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EXAMPLE_DOCS_DIRECTORY = os.path.join(
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pathlib.Path(__file__).parent.resolve(), "..", "..", "example-docs"
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)
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TESTING_FILE_DIR = os.path.join(EXAMPLE_DOCS_DIRECTORY, "test_evaluate_files")
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UNSTRUCTURED_OUTPUT_DIRNAME = "unstructured_output"
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GOLD_CCT_DIRNAME = "gold_standard_cct"
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GOLD_ELEMENT_TYPE_DIRNAME = "gold_standard_element_type"
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GOLD_TABLE_STRUCTURE_DIRNAME = "gold_standard_table_structure"
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UNSTRUCTURED_CCT_DIRNAME = "unstructured_output_cct"
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UNSTRUCTURED_TABLE_STRUCTURE_DIRNAME = "unstructured_output_table_structure"
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DUMMY_DF_CCT = pd.DataFrame(
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{
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"filename": [
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"Bank Good Credit Loan.pptx",
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"Performance-Audit-Discussion.pdf",
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"currency.csv",
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],
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"doctype": ["pptx", "pdf", "csv"],
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"connector": ["connector1", "connector1", "connector2"],
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"cct-accuracy": [0.812, 0.994, 0.887],
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"cct-%missing": [0.001, 0.002, 0.041],
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}
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)
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DUMMY_DF_ELEMENT_TYPE = pd.DataFrame(
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{
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"filename": [
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"Bank Good Credit Loan.pptx",
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"Performance-Audit-Discussion.pdf",
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"currency.csv",
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],
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"doctype": ["pptx", "pdf", "csv"],
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"connector": ["connector1", "connector1", "connector2"],
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"element-type-accuracy": [0.812, 0.994, 0.887],
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}
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)
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@pytest.fixture()
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def _cleanup_after_test():
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"""Fixture for removing side-effects of running tests in this file."""
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def remove_generated_directories():
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"""Remove directories created from running tests."""
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# Directories to be removed:
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target_dir_names = [
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"test_evaluate_results_cct",
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"test_evaluate_results_cct_txt",
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"test_evaluate_results_element_type",
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"test_evaluate_result_table_structure",
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]
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subdirs = (d for d in os.scandir(TESTING_FILE_DIR) if d.is_dir())
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for d in subdirs:
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if d.name in target_dir_names:
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shutil.rmtree(d.path)
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# Run test as normal
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yield
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remove_generated_directories()
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_text_extraction_evaluation():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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TextExtractionMetricsCalculator(
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documents_dir=output_dir, ground_truths_dir=source_dir
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).calculate(export_dir=export_dir, visualize_progress=False, display_agg_df=False)
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assert os.path.isfile(os.path.join(export_dir, "all-docs-cct.tsv"))
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df = pd.read_csv(os.path.join(export_dir, "all-docs-cct.tsv"), sep="\t")
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assert len(df) == 3
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assert len(df.columns) == 5
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assert df.iloc[0].filename == "Bank Good Credit Loan.pptx"
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@pytest.mark.parametrize(
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("calculator_class", "output_dirname", "source_dirname", "path", "expected_length", "kwargs"),
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[
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(
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TextExtractionMetricsCalculator,
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UNSTRUCTURED_CCT_DIRNAME,
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GOLD_CCT_DIRNAME,
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Path("Bank Good Credit Loan.pptx.txt"),
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5,
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{"document_type": "txt"},
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),
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(
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TableStructureMetricsCalculator,
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UNSTRUCTURED_TABLE_STRUCTURE_DIRNAME,
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GOLD_TABLE_STRUCTURE_DIRNAME,
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Path("IRS-2023-Form-1095-A.pdf.json"),
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13,
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{},
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),
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(
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ElementTypeMetricsCalculator,
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UNSTRUCTURED_OUTPUT_DIRNAME,
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GOLD_ELEMENT_TYPE_DIRNAME,
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Path("IRS-form-1987.pdf.json"),
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4,
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{},
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),
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],
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)
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def test_process_document_returns_the_correct_amount_of_values(
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calculator_class, output_dirname, source_dirname, path, expected_length, kwargs
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):
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output_dir = Path(TESTING_FILE_DIR) / output_dirname
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source_dir = Path(TESTING_FILE_DIR) / source_dirname
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calculator = calculator_class(documents_dir=output_dir, ground_truths_dir=source_dir, **kwargs)
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output_list = calculator._process_document(path)
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assert len(output_list) == expected_length
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_text_extraction_evaluation_type_txt():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_CCT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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TextExtractionMetricsCalculator(
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documents_dir=output_dir, ground_truths_dir=source_dir, document_type="txt"
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).calculate(export_dir=export_dir)
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df = pd.read_csv(os.path.join(export_dir, "all-docs-cct.tsv"), sep="\t")
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assert len(df) == 3
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assert len(df.columns) == 5
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assert df.iloc[0].filename == "Bank Good Credit Loan.pptx"
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_element_type_evaluation():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_ELEMENT_TYPE_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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ElementTypeMetricsCalculator(
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documents_dir=output_dir,
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ground_truths_dir=source_dir,
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).calculate(export_dir=export_dir, visualize_progress=False)
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assert os.path.isfile(os.path.join(export_dir, "all-docs-element-type-frequency.tsv"))
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df = pd.read_csv(os.path.join(export_dir, "all-docs-element-type-frequency.tsv"), sep="\t")
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assert len(df) == 1
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assert len(df.columns) == 4
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assert df.iloc[0].filename == "IRS-form-1987.pdf"
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_table_structure_evaluation():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_TABLE_STRUCTURE_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_TABLE_STRUCTURE_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_result_table_structure")
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TableStructureMetricsCalculator(
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documents_dir=output_dir,
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ground_truths_dir=source_dir,
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).calculate(export_dir=export_dir, visualize_progress=False)
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assert os.path.isfile(os.path.join(export_dir, "all-docs-table-structure-accuracy.tsv"))
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assert os.path.isfile(os.path.join(export_dir, "aggregate-table-structure-accuracy.tsv"))
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df = pd.read_csv(os.path.join(export_dir, "all-docs-table-structure-accuracy.tsv"), sep="\t")
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assert len(df) == 1
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assert len(df.columns) == 13
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assert df.iloc[0].filename == "IRS-2023-Form-1095-A.pdf"
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_text_extraction_takes_list():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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output_list = ["currency.csv.json"]
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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TextExtractionMetricsCalculator(
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documents_dir=output_dir,
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ground_truths_dir=source_dir,
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).on_files(document_paths=output_list).calculate(export_dir=export_dir)
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# check that only the listed files are included
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assert os.path.isfile(os.path.join(export_dir, "all-docs-cct.tsv"))
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df = pd.read_csv(os.path.join(export_dir, "all-docs-cct.tsv"), sep="\t")
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assert len(df) == len(output_list)
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_text_extraction_with_grouping():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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TextExtractionMetricsCalculator(
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documents_dir=output_dir,
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ground_truths_dir=source_dir,
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group_by="doctype",
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).calculate(export_dir=export_dir)
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df = pd.read_csv(os.path.join(export_dir, "all-doctype-agg-cct.tsv"), sep="\t")
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assert len(df) == 4 # metrics row and doctype rows
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_text_extraction_wrong_type():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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with pytest.raises(ValueError):
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TextExtractionMetricsCalculator(
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documents_dir=output_dir, ground_truths_dir=source_dir, document_type="invalid type"
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).calculate(export_dir=export_dir)
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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@pytest.mark.parametrize(("grouping", "count_row"), [("doctype", 3), ("connector", 2)])
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def test_get_mean_grouping_df_input(grouping: str, count_row: int):
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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get_mean_grouping(
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group_by=grouping,
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data_input=DUMMY_DF_CCT,
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export_dir=export_dir,
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eval_name="text_extraction",
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)
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grouped_df = pd.read_csv(os.path.join(export_dir, f"all-{grouping}-agg-cct.tsv"), sep="\t")
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assert grouped_df[grouping].dropna().nunique() == count_row
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_get_mean_grouping_tsv_input():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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TextExtractionMetricsCalculator(
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documents_dir=output_dir,
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ground_truths_dir=source_dir,
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).calculate(export_dir=export_dir)
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filename = os.path.join(export_dir, "all-docs-cct.tsv")
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get_mean_grouping(
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group_by="doctype",
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data_input=filename,
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export_dir=export_dir,
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eval_name="text_extraction",
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)
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grouped_df = pd.read_csv(os.path.join(export_dir, "all-doctype-agg-cct.tsv"), sep="\t")
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assert grouped_df["doctype"].dropna().nunique() == 3
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_get_mean_grouping_invalid_group():
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output_dir = os.path.join(TESTING_FILE_DIR, UNSTRUCTURED_OUTPUT_DIRNAME)
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source_dir = os.path.join(TESTING_FILE_DIR, GOLD_CCT_DIRNAME)
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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TextExtractionMetricsCalculator(
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documents_dir=output_dir,
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ground_truths_dir=source_dir,
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).calculate(export_dir=export_dir)
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df = pd.read_csv(os.path.join(export_dir, "all-docs-cct.tsv"), sep="\t")
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with pytest.raises(ValueError):
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get_mean_grouping(
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group_by="invalid",
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data_input=df,
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export_dir=export_dir,
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eval_name="text_extraction",
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)
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_text_extraction_grouping_empty_df():
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empty_df = pd.DataFrame()
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with pytest.raises(SystemExit):
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get_mean_grouping("doctype", empty_df, "some_dir", eval_name="text_extraction")
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_get_mean_grouping_missing_grouping_column():
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df_with_no_grouping = pd.DataFrame({"some_column": [1, 2, 3]})
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with pytest.raises(SystemExit):
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get_mean_grouping("doctype", df_with_no_grouping, "some_dir", "text_extraction")
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_get_mean_grouping_all_null_grouping_column():
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df_with_null_grouping = pd.DataFrame({"doctype": [None, None, None]})
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with pytest.raises(SystemExit):
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get_mean_grouping("doctype", df_with_null_grouping, "some_dir", eval_name="text_extraction")
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_get_mean_grouping_invalid_eval_name():
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with pytest.raises(ValueError):
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get_mean_grouping("doctype", DUMMY_DF_ELEMENT_TYPE, "some_dir", eval_name="invalid")
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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@pytest.mark.parametrize(("group_by", "count_row"), [("doctype", 3), ("connector", 2)])
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def test_get_mean_grouping_element_type(group_by: str, count_row: int):
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_element_type")
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get_mean_grouping(
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group_by=group_by,
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data_input=DUMMY_DF_ELEMENT_TYPE,
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export_dir=export_dir,
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eval_name="element_type",
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)
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grouped_df = pd.read_csv(
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os.path.join(export_dir, f"all-{group_by}-agg-element-type.tsv"), sep="\t"
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)
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assert grouped_df[group_by].dropna().nunique() == count_row
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_filter_metrics():
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with open(os.path.join(TESTING_FILE_DIR, "filter_list.txt"), "w") as file:
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file.write("Bank Good Credit Loan.pptx\n")
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file.write("Performance-Audit-Discussion.pdf\n")
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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filter_metrics(
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data_input=DUMMY_DF_CCT,
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filter_list=os.path.join(TESTING_FILE_DIR, "filter_list.txt"),
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filter_by="filename",
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export_filename="filtered_metrics.tsv",
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export_dir=export_dir,
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return_type="file",
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)
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filtered_df = pd.read_csv(os.path.join(export_dir, "filtered_metrics.tsv"), sep="\t")
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assert len(filtered_df) == 2
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assert filtered_df["filename"].iloc[0] == "Bank Good Credit Loan.pptx"
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@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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@pytest.mark.usefixtures("_cleanup_after_test")
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def test_get_mean_grouping_all_file():
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with open(os.path.join(TESTING_FILE_DIR, "filter_list.txt"), "w") as file:
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file.write("Bank Good Credit Loan.pptx\n")
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file.write("Performance-Audit-Discussion.pdf\n")
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export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
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filter_metrics(
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data_input=DUMMY_DF_CCT,
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filter_list=["Bank Good Credit Loan.pptx", "Performance-Audit-Discussion.pdf"],
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filter_by="filename",
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export_filename="filtered_metrics.tsv",
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export_dir=export_dir,
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return_type="file",
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)
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filtered_df = pd.read_csv(os.path.join(export_dir, "filtered_metrics.tsv"), sep="\t")
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get_mean_grouping(
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group_by="all",
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data_input=filtered_df,
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export_dir=export_dir,
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eval_name="text_extraction",
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export_filename="two-filename-agg-cct.tsv",
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)
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grouped_df = pd.read_csv(os.path.join(export_dir, "two-filename-agg-cct.tsv"), sep="\t")
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assert np.isclose(float(grouped_df.iloc[1, 0]), 0.903)
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assert np.isclose(float(grouped_df.iloc[1, 1]), 0.129)
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assert np.isclose(float(grouped_df.iloc[1, 2]), 0.091)
|
|
|
|
|
|
@pytest.mark.skipif(is_in_docker, reason="Skipping this test in Docker container")
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|
@pytest.mark.usefixtures("_cleanup_after_test")
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|
def test_get_mean_grouping_all_file_txt():
|
|
with open(os.path.join(TESTING_FILE_DIR, "filter_list.txt"), "w") as file:
|
|
file.write("Bank Good Credit Loan.pptx\n")
|
|
file.write("Performance-Audit-Discussion.pdf\n")
|
|
export_dir = os.path.join(TESTING_FILE_DIR, "test_evaluate_results_cct")
|
|
|
|
filter_metrics(
|
|
data_input=DUMMY_DF_CCT,
|
|
filter_list=os.path.join(TESTING_FILE_DIR, "filter_list.txt"),
|
|
filter_by="filename",
|
|
export_filename="filtered_metrics.tsv",
|
|
export_dir=export_dir,
|
|
return_type="file",
|
|
)
|
|
filtered_df = pd.read_csv(os.path.join(export_dir, "filtered_metrics.tsv"), sep="\t")
|
|
|
|
get_mean_grouping(
|
|
group_by="all",
|
|
data_input=filtered_df,
|
|
export_dir=export_dir,
|
|
eval_name="text_extraction",
|
|
export_filename="two-filename-agg-cct.tsv",
|
|
)
|
|
grouped_df = pd.read_csv(os.path.join(export_dir, "two-filename-agg-cct.tsv"), sep="\t")
|
|
|
|
assert np.isclose(float(grouped_df.iloc[1, 0]), 0.903)
|
|
assert np.isclose(float(grouped_df.iloc[1, 1]), 0.129)
|
|
assert np.isclose(float(grouped_df.iloc[1, 2]), 0.091)
|