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feat: add ocr_redo frontmatter field + sync preservation
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Research Assistant
parent
363b0cb962
commit
37768d15be
4 changed files with 176 additions and 1 deletions
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@ -380,6 +380,21 @@ def extract_preserved_tags(text: str) -> list[str] | None:
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return None
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def extract_preserved_ocr_redo(text: str) -> bool:
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"""Extract ocr_redo flag from existing note frontmatter.
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Returns True if ocr_redo is explicitly set to true in YAML frontmatter.
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Returns False otherwise (missing, unreadable, or explicitly false).
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"""
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data = read_frontmatter_dict(text)
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val = data.get("ocr_redo", False)
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if isinstance(val, bool):
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return val
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if isinstance(val, str):
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return val.strip().lower() in ("true", "yes", "1")
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return False
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def read_frontmatter_dict(text: str) -> dict:
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"""Parse YAML frontmatter from markdown text using yaml.safe_load.
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@ -128,6 +128,13 @@ frontmatter:
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owner: ocr
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default: "none"
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introduced_in: "2.1"
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ocr_redo:
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type: bool
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required: false
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public: true
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description: "User requests OCR redo"
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owner: user
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introduced_in: "1.5.14"
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deep_reading_status:
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type: enum
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values:
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@ -28,6 +28,7 @@ from paperforge.adapters.obsidian_frontmatter import (
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canonicalize_decision,
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compute_final_collection,
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extract_preserved_deep_reading,
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extract_preserved_ocr_redo,
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extract_preserved_tags,
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update_frontmatter_field,
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)
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@ -995,10 +996,12 @@ def next_key(domain: str, export_rows: list[dict]) -> str:
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return f"{prefix}{max_num + 1:03d}"
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def frontmatter_note(entry: dict, existing_text: str = "", preserved_tags: list[str] | None = None) -> str:
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def frontmatter_note(entry: dict, existing_text: str = "", preserved_tags: list[str] | None = None, preserved_ocr_redo: bool | None = None) -> str:
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preserved_deep = extract_preserved_deep_reading(existing_text)
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if preserved_tags is None and existing_text:
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preserved_tags = extract_preserved_tags(existing_text)
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if preserved_ocr_redo is None and existing_text:
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preserved_ocr_redo = extract_preserved_ocr_redo(existing_text)
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first_author = entry.get("first_author", "")
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if not first_author:
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authors = entry.get("authors", [])
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@ -1033,6 +1036,8 @@ def frontmatter_note(entry: dict, existing_text: str = "", preserved_tags: list[
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f"fulltext_md_path: {yaml_quote('[[{}]]'.format(entry['fulltext_path']) if entry.get('ocr_status') == 'done' and entry.get('fulltext_path') else '')}",
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]
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)
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if preserved_ocr_redo:
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lines.append("ocr_redo: true")
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if preserved_tags is not None:
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lines.append("tags:")
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for tag in preserved_tags:
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@ -6,6 +6,39 @@ from unittest.mock import patch
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from PIL import Image
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def test_extract_preserved_ocr_redo_preserves_flag_across_frontmatter_rewrite() -> None:
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"""Simulate sync preserving ocr_redo through frontmatter_note()."""
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from paperforge.adapters.obsidian_frontmatter import extract_preserved_ocr_redo
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from paperforge.worker.sync import frontmatter_note
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entry = {"zotero_key": "TEST", "title": "Test", "year": "2025"}
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original = """---
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zotero_key: TEST
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title: Test
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year: 2025
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ocr_redo: true
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---
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"""
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preserved = extract_preserved_ocr_redo(original)
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assert preserved is True
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rewritten = frontmatter_note(entry, existing_text=original)
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assert "ocr_redo: true" in rewritten
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def test_extract_preserved_ocr_redo_false_by_default() -> None:
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from paperforge.adapters.obsidian_frontmatter import extract_preserved_ocr_redo
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text = """---
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zotero_key: TEST
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title: Test
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---
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"""
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assert extract_preserved_ocr_redo(text) is False
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def test_caption_group_assignments_respects_columns() -> None:
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from paperforge.worker.ocr import caption_group_assignments
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@ -256,6 +289,121 @@ def test_render_page_blocks_links_media_for_text_caption(tmp_path: Path) -> None
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assert any(line.startswith("Figure 4 RT-qPCR results.") for line in rendered)
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def test_render_page_blocks_keeps_author_year_references_as_reference_items(tmp_path: Path) -> None:
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from paperforge.worker.ocr import render_page_blocks
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vault = tmp_path / "vault"
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images_dir = vault / "System" / "PaperForge" / "ocr" / "KEY" / "images"
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page_cache_dir = vault / "System" / "PaperForge" / "ocr" / "KEY" / "pages"
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images_dir.mkdir(parents=True)
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page_cache_dir.mkdir(parents=True)
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result = {
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"prunedResult": {
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"width": 1200,
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"height": 1600,
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"parsing_res_list": [
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{"block_id": 1, "block_label": "paragraph_title", "block_bbox": [90, 120, 330, 160], "block_content": "References"},
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{
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"block_id": 2,
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"block_label": "reference_content",
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"block_bbox": [90, 220, 520, 300],
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"block_content": "Amin, B., Elahi, M. A., and Porter, E. (2019). A review of dielectric properties.",
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},
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{
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"block_id": 3,
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"block_label": "reference_content",
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"block_bbox": [620, 220, 1100, 300],
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"block_content": "Barker, A. T., and Lunt, M. J. (1983). The effects of pulsed magnetic fields.",
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},
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],
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},
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"inputImage": "",
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}
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rendered = render_page_blocks(vault, 22, result, images_dir, page_cache_dir, pdf_doc=None)
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assert "### References" in rendered
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assert any(line.startswith("Amin, B., Elahi") for line in rendered)
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assert any(line.startswith("Barker, A. T.") for line in rendered)
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def test_render_page_blocks_does_not_mix_tail_sections_into_references(tmp_path: Path) -> None:
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from paperforge.worker.ocr import render_page_blocks
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vault = tmp_path / "vault"
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images_dir = vault / "System" / "PaperForge" / "ocr" / "KEY" / "images"
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page_cache_dir = vault / "System" / "PaperForge" / "ocr" / "KEY" / "pages"
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images_dir.mkdir(parents=True)
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page_cache_dir.mkdir(parents=True)
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result = {
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"prunedResult": {
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"width": 1200,
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"height": 1600,
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"parsing_res_list": [
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{"block_id": 1, "block_label": "paragraph_title", "block_bbox": [90, 120, 330, 160], "block_content": "References"},
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{
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"block_id": 2,
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"block_label": "reference_content",
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"block_bbox": [90, 220, 520, 300],
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"block_content": "Amin, B., Elahi, M. A., and Porter, E. (2019). A review of dielectric properties.",
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},
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{
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"block_id": 3,
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"block_label": "paragraph_title",
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"block_bbox": [620, 120, 1080, 160],
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"block_content": "Generative AI statement",
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},
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{
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"block_id": 4,
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"block_label": "text",
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"block_bbox": [620, 220, 1100, 280],
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"block_content": "The author(s) declare that no Generative AI was used in the creation of this manuscript.",
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},
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],
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},
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"inputImage": "",
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}
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rendered = render_page_blocks(vault, 22, result, images_dir, page_cache_dir, pdf_doc=None)
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refs_index = rendered.index("### References")
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ai_index = rendered.index("### Generative AI statement")
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assert rendered[refs_index + 1].startswith("Amin, B., Elahi")
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assert rendered[ai_index + 1].startswith("The author(s) declare")
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def test_render_page_blocks_orders_references_within_column(tmp_path: Path) -> None:
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from paperforge.worker.ocr import render_page_blocks
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vault = tmp_path / "vault"
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images_dir = vault / "System" / "PaperForge" / "ocr" / "KEY" / "images"
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page_cache_dir = vault / "System" / "PaperForge" / "ocr" / "KEY" / "pages"
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images_dir.mkdir(parents=True)
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page_cache_dir.mkdir(parents=True)
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result = {
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"prunedResult": {
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"width": 1200,
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"height": 1600,
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"parsing_res_list": [
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{"block_id": 1, "block_label": "paragraph_title", "block_bbox": [90, 120, 330, 160], "block_content": "References"},
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{"block_id": 2, "block_label": "reference_content", "block_bbox": [620, 200, 1100, 250], "block_content": "Bagnato, G. L. (2016)."},
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{"block_id": 3, "block_label": "reference_content", "block_bbox": [90, 200, 520, 250], "block_content": "Amin, B. (2019)."},
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{"block_id": 4, "block_label": "reference_content", "block_bbox": [90, 300, 520, 350], "block_content": "Cai, J. (2018)."},
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{"block_id": 5, "block_label": "reference_content", "block_bbox": [620, 300, 1100, 350], "block_content": "Bentley, G. (2012)."},
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],
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},
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"inputImage": "",
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}
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rendered = render_page_blocks(vault, 22, result, images_dir, page_cache_dir, pdf_doc=None)
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ref_items = [line for line in rendered if line.startswith(("Amin", "Cai", "Bagnato", "Bentley"))]
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assert ref_items == ["Amin, B. (2019).", "Cai, J. (2018).", "Bagnato, G. L. (2016).", "Bentley, G. (2012)."]
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def test_embedded_figure_text_excludes_body_paragraph_like_text() -> None:
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from paperforge.worker.ocr import is_embedded_figure_text_block
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