1ac010354f
* test: avoid testing exact JSON Avoid testing exact JSON output in html and xml backends. Reuse the JSON verify helper function among backend test files. Improve type annotations in html backend. Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> * Update tests/test_backend_patent_uspto.py Co-authored-by: Michele Dolfi <97102151+dolfim-ibm@users.noreply.github.com> Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> --------- Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> Co-authored-by: Michele Dolfi <97102151+dolfim-ibm@users.noreply.github.com>
458 lines
20 KiB
Python
458 lines
20 KiB
Python
"""Test methods in module docling.backend.patent_uspto_backend.py."""
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import logging
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import os
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from pathlib import Path
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from tempfile import NamedTemporaryFile
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import pytest
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from docling_core.types import DoclingDocument
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from docling_core.types.doc import DocItemLabel, TableData, TextItem
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from docling.backend.xml.uspto_backend import PatentUsptoDocumentBackend, XmlTable
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from docling.datamodel.base_models import InputFormat
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from docling.datamodel.document import InputDocument
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from .verify_utils import verify_document
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GENERATE: bool = False
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DATA_PATH: Path = Path("./tests/data/uspto/")
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GT_PATH: Path = Path("./tests/data/groundtruth/docling_v2/")
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def _generate_groundtruth(doc: DoclingDocument, file_stem: str) -> None:
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with open(GT_PATH / f"{file_stem}.itxt", "w", encoding="utf-8") as file_obj:
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file_obj.write(doc._export_to_indented_text())
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doc.save_as_json(GT_PATH / f"{file_stem}.json")
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doc.save_as_markdown(GT_PATH / f"{file_stem}.md")
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@pytest.fixture(scope="module")
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def patents() -> list[tuple[Path, DoclingDocument]]:
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patent_paths = (
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sorted(DATA_PATH.glob("ip*.xml"))
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+ sorted(DATA_PATH.glob("pg*.xml"))
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+ sorted(DATA_PATH.glob("pa*.xml"))
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+ sorted(DATA_PATH.glob("pftaps*.txt"))
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)
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patents: list[dict[Path, DoclingDocument]] = []
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for in_path in patent_paths:
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in_doc = InputDocument(
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path_or_stream=in_path,
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format=InputFormat.XML_USPTO,
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backend=PatentUsptoDocumentBackend,
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)
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backend = PatentUsptoDocumentBackend(in_doc=in_doc, path_or_stream=in_path)
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logging.info(f"Converting patent from file {in_path}")
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doc = backend.convert()
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assert doc, f"Failed to parse document {in_path}"
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patents.append((in_path, doc))
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return patents
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@pytest.fixture(scope="module")
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def groundtruth() -> list[tuple[Path, str]]:
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patent_paths = (
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sorted(GT_PATH.glob("ip*"))
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+ sorted(GT_PATH.glob("pg*"))
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+ sorted(GT_PATH.glob("pa*"))
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+ sorted(GT_PATH.glob("pftaps*"))
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)
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groundtruth: list[tuple[Path, str]] = []
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for in_path in patent_paths:
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with open(in_path, encoding="utf-8") as file_obj:
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content = file_obj.read()
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groundtruth.append((in_path, content))
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return groundtruth
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@pytest.fixture(scope="module")
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def tables() -> list[tuple[Path, TableData]]:
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table_paths = sorted(DATA_PATH.glob("tables*.xml"))
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tables: list[tuple[Path, TableData]] = []
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for in_path in table_paths:
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with open(in_path, encoding="utf-8") as file_obj:
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content = file_obj.read()
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parser = XmlTable(content)
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parsed_table = parser.parse()
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assert parsed_table
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tables.append((in_path, parsed_table))
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return tables
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@pytest.mark.skip("Slow test")
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def test_patent_export(patents):
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for _, doc in patents:
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with NamedTemporaryFile(suffix=".yaml", delete=False) as tmp_file:
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doc.save_as_yaml(Path(tmp_file.name))
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assert os.path.getsize(tmp_file.name) > 0
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with NamedTemporaryFile(suffix=".html", delete=False) as tmp_file:
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doc.save_as_html(Path(tmp_file.name))
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assert os.path.getsize(tmp_file.name) > 0
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with NamedTemporaryFile(suffix=".md", delete=False) as tmp_file:
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doc.save_as_markdown(Path(tmp_file.name))
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assert os.path.getsize(tmp_file.name) > 0
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def test_patent_groundtruth(patents, groundtruth):
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gt_stems: list[str] = [item[0].stem for item in groundtruth]
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gt_names: dict[str, str] = {item[0].name: item[1] for item in groundtruth}
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for path, doc in patents:
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if path.stem not in gt_stems:
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continue
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md_name = path.stem + ".md"
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if md_name in gt_names:
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pred_md = doc.export_to_markdown()
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assert (
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pred_md == gt_names[md_name]
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), f"Markdown file mismatch against groundtruth {md_name}"
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json_path = path.with_suffix(".json")
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if json_path.stem in gt_names:
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assert verify_document(
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doc, str(json_path), GENERATE
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), f"JSON file mismatch against groundtruth {json_path}"
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itxt_name = path.stem + ".itxt"
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if itxt_name in gt_names:
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pred_itxt = doc._export_to_indented_text()
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assert (
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pred_itxt == gt_names[itxt_name]
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), f"Indented text file mismatch against groundtruth {itxt_name}"
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def test_tables(tables):
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"""Test the table parser."""
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# CHECK table in file tables_20180000016.xml
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file_name = "tables_ipa20180000016.xml"
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file_table = [item[1] for item in tables if item[0].name == file_name][0]
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assert file_table.num_rows == 13
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assert file_table.num_cols == 10
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assert len(file_table.table_cells) == 130
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def test_patent_uspto_ice(patents):
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"""Test applications and grants Full Text Data/XML Version 4.x ICE."""
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# CHECK application doc number 20200022300
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file_name = "ipa20200022300.xml"
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doc = [item[1] for item in patents if item[0].name == file_name][0]
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if GENERATE:
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_generate_groundtruth(doc, Path(file_name).stem)
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assert doc.name == file_name
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texts = doc.texts
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assert len(texts) == 78
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assert isinstance(texts[0], TextItem)
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assert (
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texts[0].text
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== "SYSTEM FOR CONTROLLING THE OPERATION OF AN ACTUATOR MOUNTED ON A SEED PLANTING IMPLEMENT"
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)
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assert texts[0].label == DocItemLabel.TITLE
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assert texts[0].parent.cref == "#/body"
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assert isinstance(texts[1], TextItem)
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assert texts[1].text == "ABSTRACT"
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assert texts[1].label == DocItemLabel.SECTION_HEADER
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assert texts[1].parent.cref == "#/texts/0"
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assert isinstance(texts[2], TextItem)
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assert texts[2].text == (
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"In one aspect, a system for controlling an operation of an actuator mounted "
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"on a seed planting implement may include an actuator configured to adjust a "
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"position of a row unit of the seed planting implement relative to a toolbar "
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"of the seed planting implement. The system may also include a flow restrictor"
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" fluidly coupled to a fluid chamber of the actuator, with the flow restrictor"
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" being configured to reduce a rate at which fluid is permitted to exit the "
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"fluid chamber in a manner that provides damping to the row unit. Furthermore,"
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" the system may include a valve fluidly coupled to the flow restrictor in a "
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"parallel relationship such that the valve is configured to permit the fluid "
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"exiting the fluid chamber to flow through the flow restrictor and the fluid "
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"entering the fluid chamber to bypass the flow restrictor."
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)
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assert texts[2].label == DocItemLabel.PARAGRAPH
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assert texts[2].parent.cref == "#/texts/1"
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assert isinstance(texts[3], TextItem)
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assert texts[3].text == "FIELD"
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assert texts[3].label == DocItemLabel.SECTION_HEADER
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assert texts[3].parent.cref == "#/texts/0"
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assert isinstance(texts[4], TextItem)
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assert texts[4].text == (
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"The present disclosure generally relates to seed planting implements and, "
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"more particularly, to systems for controlling the operation of an actuator "
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"mounted on a seed planting implement in a manner that provides damping to "
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"one or more components of the seed planting implement."
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)
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assert texts[4].label == DocItemLabel.PARAGRAPH
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assert texts[4].parent.cref == "#/texts/3"
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assert isinstance(texts[5], TextItem)
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assert texts[5].text == "BACKGROUND"
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assert texts[5].label == DocItemLabel.SECTION_HEADER
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assert texts[5].parent.cref == "#/texts/0"
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assert isinstance(texts[6], TextItem)
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assert texts[6].text == (
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"Modern farming practices strive to increase yields of agricultural fields. In"
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" this respect, seed planting implements are towed behind a tractor or other "
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"work vehicle to deposit seeds in a field. For example, seed planting "
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"implements typically include one or more ground engaging tools or openers "
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"that form a furrow or trench in the soil. One or more dispensing devices of "
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"the seed planting implement may, in turn, deposit seeds into the furrow(s). "
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"After deposition of the seeds, a packer wheel may pack the soil on top of the"
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" deposited seeds."
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)
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assert texts[6].label == DocItemLabel.PARAGRAPH
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assert texts[6].parent.cref == "#/texts/5"
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assert isinstance(texts[7], TextItem)
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assert texts[7].text == (
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"In certain instances, the packer wheel may also control the penetration depth"
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" of the furrow. In this regard, the position of the packer wheel may be moved"
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" vertically relative to the associated opener(s) to adjust the depth of the "
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"furrow. Additionally, the seed planting implement includes an actuator "
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"configured to exert a downward force on the opener(s) to ensure that the "
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"opener(s) is able to penetrate the soil to the depth set by the packer wheel."
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" However, the seed planting implement may bounce or chatter when traveling at"
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" high speeds and/or when the opener(s) encounters hard or compacted soil. As "
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"such, operators generally operate the seed planting implement with the "
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"actuator exerting more downward force on the opener(s) than is necessary in "
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"order to prevent such bouncing or chatter. Operation of the seed planting "
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"implement with excessive down pressure applied to the opener(s), however, "
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"reduces the overall stability of the seed planting implement."
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)
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assert texts[7].label == DocItemLabel.PARAGRAPH
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assert texts[7].parent.cref == "#/texts/5"
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assert isinstance(texts[8], TextItem)
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assert texts[8].text == (
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"Accordingly, an improved system for controlling the operation of an actuator "
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"mounted on s seed planting implement to enhance the overall operation of the "
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"implement would be welcomed in the technology."
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)
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assert texts[8].label == DocItemLabel.PARAGRAPH
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assert texts[8].parent.cref == "#/texts/5"
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assert isinstance(texts[9], TextItem)
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assert texts[9].text == "BRIEF DESCRIPTION"
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assert texts[9].label == DocItemLabel.SECTION_HEADER
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assert texts[9].parent.cref == "#/texts/0"
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assert isinstance(texts[15], TextItem)
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assert texts[15].text == "BRIEF DESCRIPTION OF THE DRAWINGS"
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assert texts[15].label == DocItemLabel.SECTION_HEADER
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assert texts[15].parent.cref == "#/texts/0"
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assert isinstance(texts[17], TextItem)
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assert texts[17].text == (
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"FIG. 1 illustrates a perspective view of one embodiment of a seed planting "
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"implement in accordance with aspects of the present subject matter;"
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)
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assert texts[17].label == DocItemLabel.PARAGRAPH
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assert texts[17].parent.cref == "#/texts/15"
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assert isinstance(texts[27], TextItem)
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assert texts[27].text == "DETAILED DESCRIPTION"
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assert texts[27].label == DocItemLabel.SECTION_HEADER
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assert texts[27].parent.cref == "#/texts/0"
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assert isinstance(texts[57], TextItem)
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assert texts[57].text == (
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"This written description uses examples to disclose the technology, including "
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"the best mode, and also to enable any person skilled in the art to practice "
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"the technology, including making and using any devices or systems and "
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"performing any incorporated methods. The patentable scope of the technology "
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"is defined by the claims, and may include other examples that occur to those "
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"skilled in the art. Such other examples are intended to be within the scope "
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"of the claims if they include structural elements that do not differ from the"
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" literal language of the claims, or if they include equivalent structural "
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"elements with insubstantial differences from the literal language of the "
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"claims."
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)
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assert texts[57].label == DocItemLabel.PARAGRAPH
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assert texts[57].parent.cref == "#/texts/27"
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assert isinstance(texts[58], TextItem)
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assert texts[58].text == "CLAIMS"
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assert texts[58].label == DocItemLabel.SECTION_HEADER
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assert texts[58].parent.cref == "#/texts/0"
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assert isinstance(texts[77], TextItem)
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assert texts[77].text == (
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"19. The system of claim 18, wherein the flow restrictor and the valve are "
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"fluidly coupled in a parallel relationship."
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)
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assert texts[77].label == DocItemLabel.PARAGRAPH
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assert texts[77].parent.cref == "#/texts/58"
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# CHECK application doc number 20180000016 for HTML entities, level 2 headings, tables
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file_name = "ipa20180000016.xml"
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doc = [item[1] for item in patents if item[0].name == file_name][0]
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if GENERATE:
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_generate_groundtruth(doc, Path(file_name).stem)
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assert doc.name == file_name
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texts = doc.texts
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assert len(texts) == 183
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assert isinstance(texts[0], TextItem)
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assert texts[0].text == "LIGHT EMITTING DEVICE AND PLANT CULTIVATION METHOD"
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assert texts[0].label == DocItemLabel.TITLE
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assert texts[0].parent.cref == "#/body"
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assert isinstance(texts[1], TextItem)
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assert texts[1].text == "ABSTRACT"
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assert texts[1].label == DocItemLabel.SECTION_HEADER
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assert texts[1].parent.cref == "#/texts/0"
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assert isinstance(texts[2], TextItem)
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assert texts[2].text == (
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"Provided is a light emitting device that includes a light emitting element "
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"having a light emission peak wavelength ranging from 380 nm to 490 nm, and a "
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"fluorescent material excited by light from the light emitting element and "
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"emitting light having at a light emission peak wavelength ranging from 580 nm"
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" or more to less than 680 nm. The light emitting device emits light having a "
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"ratio R/B of a photon flux density R to a photon flux density B ranging from "
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"2.0 to 4.0 and a ratio R/FR of the photon flux density R to a photon flux "
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"density FR ranging from 0.7 to 13.0, the photon flux density R being in a "
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"wavelength range of 620 nm or more and less than 700 nm, the photon flux "
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"density B being in a wavelength range of 380 nm or more and 490 nm or less, "
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"and the photon flux density FR being in a wavelength range of 700 nm or more "
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"and 780 nm or less."
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)
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assert isinstance(texts[3], TextItem)
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assert texts[3].text == "CROSS-REFERENCE TO RELATED APPLICATION"
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assert texts[3].label == DocItemLabel.SECTION_HEADER
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assert texts[3].parent.cref == "#/texts/0"
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assert isinstance(texts[4], TextItem)
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assert texts[5].text == "BACKGROUND"
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assert texts[5].label == DocItemLabel.SECTION_HEADER
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assert texts[5].parent.cref == "#/texts/0"
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assert isinstance(texts[6], TextItem)
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assert texts[6].text == "Technical Field"
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assert texts[6].label == DocItemLabel.SECTION_HEADER
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assert texts[6].parent.cref == "#/texts/0"
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assert isinstance(texts[7], TextItem)
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assert texts[7].text == (
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"The present disclosure relates to a light emitting device and a plant "
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"cultivation method."
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)
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assert texts[7].label == DocItemLabel.PARAGRAPH
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assert texts[7].parent.cref == "#/texts/6"
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assert isinstance(texts[8], TextItem)
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assert texts[8].text == "Description of Related Art"
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assert texts[8].label == DocItemLabel.SECTION_HEADER
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assert texts[8].parent.cref == "#/texts/0"
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assert isinstance(texts[63], TextItem)
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assert texts[63].text == (
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"wherein r, s, and t are numbers satisfying 0≦r≦1.0, 0≦s≦1.0, 0<t<1.0, and "
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"r+s+t≦1.0."
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)
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assert texts[63].label == DocItemLabel.PARAGRAPH
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assert texts[63].parent.cref == "#/texts/51"
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assert isinstance(texts[89], TextItem)
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assert texts[89].text == (
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"Examples of the compound containing Al, Ga, or In specifically include Al₂O₃, "
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"Ga₂O₃, and In₂O₃."
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)
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assert texts[89].label == DocItemLabel.PARAGRAPH
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assert texts[89].parent.cref == "#/texts/87"
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# CHECK application doc number 20110039701 for complex long tables
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file_name = "ipa20110039701.xml"
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doc = [item[1] for item in patents if item[0].name == file_name][0]
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assert doc.name == file_name
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assert len(doc.tables) == 17
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def test_patent_uspto_grant_v2(patents):
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"""Test applications and grants Full Text Data/APS."""
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# CHECK application doc number 06442728
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file_name = "pg06442728.xml"
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doc = [item[1] for item in patents if item[0].name == file_name][0]
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if GENERATE:
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_generate_groundtruth(doc, Path(file_name).stem)
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assert doc.name == file_name
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texts = doc.texts
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assert len(texts) == 108
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assert isinstance(texts[0], TextItem)
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assert texts[0].text == "Methods and apparatus for turbo code"
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assert texts[0].label == DocItemLabel.TITLE
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assert texts[0].parent.cref == "#/body"
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assert isinstance(texts[1], TextItem)
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assert texts[1].text == "ABSTRACT"
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assert texts[1].label == DocItemLabel.SECTION_HEADER
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assert texts[1].parent.cref == "#/texts/0"
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assert isinstance(texts[2], TextItem)
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assert texts[2].text == (
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"An interleaver receives incoming data frames of size N. The interleaver "
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"indexes the elements of the frame with an N₁×N₂ index array. The interleaver "
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"then effectively rearranges (permutes) the data by permuting the rows of the "
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"index array. The interleaver employs the equation I(j,k)=I(j,αjk+βj)modP) to "
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"permute the columns (indexed by k) of each row (indexed by j). P is at least "
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"equal to N₂, βj is a constant which may be different for each row, and each "
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"αj is a relative prime number relative to P. After permuting, the "
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"interleaver outputs the data in a different order than received (e.g., "
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"receives sequentially row by row, outputs sequentially each column by column)."
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)
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# check that the formula has been skipped
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assert texts[43].text == (
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"Calculating the specified equation with the specified values for permuting "
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"row 0 of array D 350 into row 0 of array D₁ 360 proceeds as:"
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)
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assert texts[44].text == (
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"and the permuted data frame is contained in array D₁ 360 shown in FIG. 3. "
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"Outputting the array column by column outputs the frame elements in the "
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"order:"
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)
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def test_patent_uspto_app_v1(patents):
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"""Test applications Full Text Data/XML Version 1.x."""
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# CHECK application doc number 20010031492
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file_name = "pa20010031492.xml"
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doc = [item[1] for item in patents if item[0].name == file_name][0]
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if GENERATE:
|
||
_generate_groundtruth(doc, Path(file_name).stem)
|
||
|
||
assert doc.name == file_name
|
||
texts = doc.texts
|
||
assert len(texts) == 103
|
||
assert isinstance(texts[0], TextItem)
|
||
assert texts[0].text == "Assay reagent"
|
||
assert texts[0].label == DocItemLabel.TITLE
|
||
assert texts[0].parent.cref == "#/body"
|
||
assert isinstance(texts[1], TextItem)
|
||
assert texts[1].text == "ABSTRACT"
|
||
assert texts[1].label == DocItemLabel.SECTION_HEADER
|
||
assert texts[1].parent.cref == "#/texts/0"
|
||
# check that the formula has been skipped
|
||
assert texts[62].text == (
|
||
"5. The % toxic effect for each sample was calculated as follows:"
|
||
)
|
||
assert texts[63].text == "where: Cₒ=light in control at time zero"
|
||
assert len(doc.tables) == 1
|
||
assert doc.tables[0].data.num_rows == 6
|
||
assert doc.tables[0].data.num_cols == 3
|
||
|
||
|
||
def test_patent_uspto_grant_aps(patents):
|
||
"""Test applications Full Text Data/APS."""
|
||
|
||
# CHECK application doc number 057006474
|
||
file_name = "pftaps057006474.txt"
|
||
doc = [item[1] for item in patents if item[0].name == file_name][0]
|
||
if GENERATE:
|
||
_generate_groundtruth(doc, Path(file_name).stem)
|
||
|
||
assert doc.name == file_name
|
||
texts = doc.texts
|
||
assert len(texts) == 75
|
||
assert isinstance(texts[0], TextItem)
|
||
assert texts[0].text == "Carbocation containing cyanine-type dye"
|
||
assert texts[0].label == DocItemLabel.TITLE
|
||
assert texts[0].parent.cref == "#/body"
|
||
assert isinstance(texts[1], TextItem)
|
||
assert texts[1].text == "ABSTRACT"
|
||
assert texts[1].label == DocItemLabel.SECTION_HEADER
|
||
assert texts[1].parent.cref == "#/texts/0"
|
||
assert isinstance(texts[2], TextItem)
|
||
assert texts[2].text == (
|
||
"To provide a reagent with excellent stability under storage, which can detect"
|
||
" a subject compound to be measured with higher specificity and sensitibity. "
|
||
"Complexes of a compound represented by the general formula (IV):"
|
||
)
|
||
assert len(doc.tables) == 0
|
||
for item in texts:
|
||
assert "##STR1##" not in item.text
|