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from __future__ import annotations
from pathlib import Path
from unittest . mock import patch
from PIL import Image
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def test_extract_preserved_ocr_redo_preserves_flag_across_frontmatter_rewrite ( ) - > None :
""" Simulate sync preserving ocr_redo through frontmatter_note(). """
from paperforge . adapters . obsidian_frontmatter import extract_preserved_ocr_redo
from paperforge . worker . sync import frontmatter_note
entry = { " zotero_key " : " TEST " , " title " : " Test " , " year " : " 2025 " }
original = """ ---
zotero_key : TEST
title : Test
year : 2025
ocr_redo : true
- - -
"""
preserved = extract_preserved_ocr_redo ( original )
assert preserved is True
rewritten = frontmatter_note ( entry , existing_text = original )
assert " ocr_redo: true " in rewritten
def test_extract_preserved_ocr_redo_false_by_default ( ) - > None :
from paperforge . adapters . obsidian_frontmatter import extract_preserved_ocr_redo
text = """ ---
zotero_key : TEST
title : Test
- - -
"""
assert extract_preserved_ocr_redo ( text ) is False
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def test_caption_group_assignments_respects_columns ( ) - > None :
from paperforge . worker . ocr import caption_group_assignments
blocks = [
{
" block_id " : 1 ,
" block_label " : " chart " ,
" block_bbox " : [ 80 , 116 , 546 , 434 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 2 ,
" block_label " : " figure_title " ,
" block_bbox " : [ 66 , 446 , 559 , 628 ] ,
" block_content " : " Figure 1. Left column figure. " ,
} ,
{
" block_id " : 3 ,
" block_label " : " chart " ,
" block_bbox " : [ 598 , 114 , 1063 , 493 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 4 ,
" block_label " : " figure_title " ,
" block_bbox " : [ 584 , 503 , 1079 , 744 ] ,
" block_content " : " Figure 2. Right column figure. " ,
} ,
]
figure_map , _table_map = caption_group_assignments ( blocks )
left_ids = [ item [ " block_id " ] for item in figure_map [ 2 ] ]
right_ids = [ item [ " block_id " ] for item in figure_map [ 4 ] ]
assert left_ids == [ 1 ]
assert right_ids == [ 3 ]
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def test_validate_block_order_falls_back_to_column_major_on_excessive_switches ( ) - > None :
from paperforge . worker . ocr import validate_block_order
blocks = [
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{
" block_id " : 1 ,
" block_label " : " text " ,
" block_order " : 0 ,
" block_bbox " : [ 80 , 100 , 500 , 140 ] ,
" block_content " : " L1 " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_order " : 1 ,
" block_bbox " : [ 700 , 110 , 1120 , 150 ] ,
" block_content " : " R1 " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_order " : 2 ,
" block_bbox " : [ 80 , 200 , 500 , 240 ] ,
" block_content " : " L2 " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 3 ,
" block_bbox " : [ 700 , 210 , 1120 , 250 ] ,
" block_content " : " R2 " ,
} ,
{
" block_id " : 5 ,
" block_label " : " text " ,
" block_order " : 4 ,
" block_bbox " : [ 80 , 300 , 500 , 340 ] ,
" block_content " : " L3 " ,
} ,
{
" block_id " : 6 ,
" block_label " : " text " ,
" block_order " : 5 ,
" block_bbox " : [ 700 , 310 , 1120 , 350 ] ,
" block_content " : " R3 " ,
} ,
{
" block_id " : 7 ,
" block_label " : " text " ,
" block_order " : 6 ,
" block_bbox " : [ 80 , 400 , 500 , 440 ] ,
" block_content " : " L4 " ,
} ,
{
" block_id " : 8 ,
" block_label " : " text " ,
" block_order " : 7 ,
" block_bbox " : [ 700 , 410 , 1120 , 450 ] ,
" block_content " : " R4 " ,
} ,
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]
ordered = validate_block_order ( blocks , page_width = 1200 )
assert [ block [ " block_content " ] for block in ordered ] == [ " L1 " , " L2 " , " L3 " , " L4 " , " R1 " , " R2 " , " R3 " , " R4 " ]
def test_validate_block_order_repairs_non_monotonic_order_within_column ( ) - > None :
from paperforge . worker . ocr import validate_block_order
blocks = [
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{
" block_id " : 1 ,
" block_label " : " text " ,
" block_order " : 0 ,
" block_bbox " : [ 80 , 100 , 500 , 140 ] ,
" block_content " : " L1 " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_order " : 1 ,
" block_bbox " : [ 80 , 300 , 500 , 340 ] ,
" block_content " : " L3 " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_order " : 2 ,
" block_bbox " : [ 80 , 200 , 500 , 240 ] ,
" block_content " : " L2 " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 3 ,
" block_bbox " : [ 700 , 150 , 1120 , 190 ] ,
" block_content " : " R1 " ,
} ,
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]
ordered = validate_block_order ( blocks , page_width = 1200 )
assert [ block [ " block_content " ] for block in ordered ] == [ " L1 " , " L2 " , " L3 " , " R1 " ]
def test_validate_block_order_keeps_bbox_sort_when_block_order_missing ( ) - > None :
from paperforge . worker . ocr import block_sort_key , validate_block_order
blocks = [
{ " block_id " : 1 , " block_label " : " text " , " block_bbox " : [ 700 , 300 , 1120 , 340 ] , " block_content " : " R2 " } ,
{ " block_id " : 2 , " block_label " : " text " , " block_bbox " : [ 80 , 100 , 500 , 140 ] , " block_content " : " L1 " } ,
{ " block_id " : 3 , " block_label " : " text " , " block_bbox " : [ 700 , 100 , 1120 , 140 ] , " block_content " : " R1 " } ,
{ " block_id " : 4 , " block_label " : " text " , " block_bbox " : [ 80 , 300 , 500 , 340 ] , " block_content " : " L2 " } ,
]
ordered = validate_block_order ( sorted ( blocks , key = block_sort_key ) , page_width = 0 )
assert [ block [ " block_content " ] for block in ordered ] == [ " L1 " , " R1 " , " L2 " , " R2 " ]
def test_validate_block_order_preserves_center_spanning_blocks ( ) - > None :
from paperforge . worker . ocr import validate_block_order
blocks = [
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{
" block_id " : 1 ,
" block_label " : " text " ,
" block_order " : 0 ,
" block_bbox " : [ 120 , 80 , 1080 , 140 ] ,
" block_content " : " Full-width section heading " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_order " : 1 ,
" block_bbox " : [ 80 , 180 , 500 , 240 ] ,
" block_content " : " Left paragraph one " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_order " : 2 ,
" block_bbox " : [ 700 , 190 , 1120 , 250 ] ,
" block_content " : " Right paragraph one " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 3 ,
" block_bbox " : [ 80 , 280 , 500 , 340 ] ,
" block_content " : " Left paragraph two " ,
} ,
{
" block_id " : 5 ,
" block_label " : " text " ,
" block_order " : 4 ,
" block_bbox " : [ 700 , 290 , 1120 , 350 ] ,
" block_content " : " Right paragraph two " ,
} ,
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]
ordered = validate_block_order ( blocks , page_width = 1200 )
assert [ block [ " block_content " ] for block in ordered ] == [
" Full-width section heading " ,
" Left paragraph one " ,
" Right paragraph one " ,
" Left paragraph two " ,
" Right paragraph two " ,
]
def test_validate_block_order_retains_blocks_with_invalid_bbox ( ) - > None :
from paperforge . worker . ocr import validate_block_order
blocks = [
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{
" block_id " : 1 ,
" block_label " : " text " ,
" block_order " : 0 ,
" block_bbox " : [ 80 , 100 , 500 , 140 ] ,
" block_content " : " Left valid " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_order " : 1 ,
" block_bbox " : [ 500 , 160 , 500 , 200 ] ,
" block_content " : " Broken bbox " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_order " : 2 ,
" block_bbox " : [ 700 , 180 , 1120 , 220 ] ,
" block_content " : " Right valid " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 3 ,
" block_bbox " : [ 80 , 260 , 500 , 300 ] ,
" block_content " : " Left lower " ,
} ,
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]
ordered = validate_block_order ( blocks , page_width = 1200 )
assert [ block [ " block_content " ] for block in ordered ] == [ " Left valid " , " Broken bbox " , " Right valid " , " Left lower " ]
def test_render_page_blocks_reorders_interleaved_two_column_text_by_geometry ( tmp_path : Path ) - > None :
from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" parsing_res_list " : [
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{
" block_id " : 1 ,
" block_label " : " text " ,
" block_order " : 0 ,
" block_bbox " : [ 80 , 100 , 500 , 160 ] ,
" block_content " : " Left intro paragraph with enough body text. " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_order " : 1 ,
" block_bbox " : [ 700 , 110 , 1120 , 170 ] ,
" block_content " : " Right intro paragraph with enough body text. " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_order " : 2 ,
" block_bbox " : [ 80 , 200 , 500 , 260 ] ,
" block_content " : " Left methods paragraph with enough body text. " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 3 ,
" block_bbox " : [ 700 , 210 , 1120 , 270 ] ,
" block_content " : " Right methods paragraph with enough body text. " ,
} ,
{
" block_id " : 5 ,
" block_label " : " text " ,
" block_order " : 4 ,
" block_bbox " : [ 80 , 300 , 500 , 360 ] ,
" block_content " : " Left results paragraph with enough body text. " ,
} ,
{
" block_id " : 6 ,
" block_label " : " text " ,
" block_order " : 5 ,
" block_bbox " : [ 700 , 310 , 1120 , 370 ] ,
" block_content " : " Right results paragraph with enough body text. " ,
} ,
{
" block_id " : 7 ,
" block_label " : " text " ,
" block_order " : 6 ,
" block_bbox " : [ 80 , 400 , 500 , 460 ] ,
" block_content " : " Left discussion paragraph with enough body text. " ,
} ,
{
" block_id " : 8 ,
" block_label " : " text " ,
" block_order " : 7 ,
" block_bbox " : [ 700 , 410 , 1120 , 470 ] ,
" block_content " : " Right discussion paragraph with enough body text. " ,
} ,
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] ,
} ,
" inputImage " : " " ,
}
rendered = render_page_blocks ( vault , 2 , result , images_dir , page_cache_dir , pdf_doc = None )
body_lines = [ line for line in rendered if line and not line . startswith ( " <!-- page " ) ]
assert body_lines == [
" Left intro paragraph with enough body text. " ,
" Left methods paragraph with enough body text. " ,
" Left results paragraph with enough body text. " ,
" Left discussion paragraph with enough body text. " ,
" Right intro paragraph with enough body text. " ,
" Right methods paragraph with enough body text. " ,
" Right results paragraph with enough body text. " ,
" Right discussion paragraph with enough body text. " ,
]
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def test_render_page_blocks_links_media_for_text_caption ( tmp_path : Path ) - > None :
from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
page_image = page_cache_dir / " page_009.png "
Image . new ( " RGB " , ( 1200 , 1600 ) , color = " white " ) . save ( page_image )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" parsing_res_list " : [
{
" block_id " : 1 ,
" block_label " : " vision_footnote " ,
" block_bbox " : [ 449 , 168 , 738 , 219 ] ,
" block_content " : " No Electrical Stimulation \n Electrical Stimulation 100 mV/mm " ,
} ,
{
" block_id " : 2 ,
" block_label " : " chart " ,
" block_bbox " : [ 429 , 237 , 733 , 485 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 3 ,
" block_label " : " chart " ,
" block_bbox " : [ 772 , 238 , 1071 , 484 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 4 ,
" block_label " : " chart " ,
" block_bbox " : [ 363 , 504 , 742 , 757 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 5 ,
" block_label " : " chart " ,
" block_bbox " : [ 766 , 503 , 1075 , 750 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 6 ,
" block_label " : " chart " ,
" block_bbox " : [ 428 , 774 , 729 , 1016 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 7 ,
" block_label " : " chart " ,
" block_bbox " : [ 765 , 768 , 1075 , 1013 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 8 ,
" block_label " : " figure_title " ,
" block_bbox " : [ 374 , 1046 , 1143 , 1077 ] ,
" block_content " : " Days post culture in osteogenic differentiation supplemented medium " ,
} ,
{
" block_id " : 9 ,
" block_label " : " text " ,
" block_bbox " : [ 373 , 1101 , 1143 , 1258 ] ,
" block_content " : " Figure 4 RT-qPCR results. Temporal changes in messenger RNA (mRNA) of (A) Runx2, (B) Osteopontin and (C) Col1A2. " ,
} ,
] ,
} ,
" inputImage " : " " ,
}
with patch ( " paperforge.worker.ocr.render_pdf_page_cached " , return_value = page_image ) :
rendered = render_page_blocks ( vault , 9 , result , images_dir , page_cache_dir , pdf_doc = None )
assert any ( line . startswith ( " ![[ " ) for line in rendered )
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 :
from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" 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 " : [ 90 , 220 , 520 , 300 ] ,
" block_content " : " Amin, B., Elahi, M. A., and Porter, E. (2019). A review of dielectric properties. " ,
} ,
{
" block_id " : 3 ,
" block_label " : " reference_content " ,
" block_bbox " : [ 620 , 220 , 1100 , 300 ] ,
" block_content " : " Barker, A. T., and Lunt, M. J. (1983). The effects of pulsed magnetic fields. " ,
} ,
] ,
} ,
" inputImage " : " " ,
}
rendered = render_page_blocks ( vault , 22 , result , images_dir , page_cache_dir , pdf_doc = None )
assert " ### References " in rendered
assert any ( line . startswith ( " Amin, B., Elahi " ) for line in rendered )
assert any ( line . startswith ( " Barker, A. T. " ) for line in rendered )
def test_render_page_blocks_does_not_mix_tail_sections_into_references ( tmp_path : Path ) - > None :
from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" 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 " : [ 90 , 220 , 520 , 300 ] ,
" block_content " : " Amin, B., Elahi, M. A., and Porter, E. (2019). A review of dielectric properties. " ,
} ,
{
" block_id " : 3 ,
" block_label " : " paragraph_title " ,
" block_bbox " : [ 620 , 120 , 1080 , 160 ] ,
" block_content " : " Generative AI statement " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_bbox " : [ 620 , 220 , 1100 , 280 ] ,
" block_content " : " The author(s) declare that no Generative AI was used in the creation of this manuscript. " ,
} ,
] ,
} ,
" inputImage " : " " ,
}
rendered = render_page_blocks ( vault , 22 , result , images_dir , page_cache_dir , pdf_doc = None )
refs_index = rendered . index ( " ### References " )
ai_index = rendered . index ( " ### Generative AI statement " )
assert rendered [ refs_index + 1 ] . startswith ( " Amin, B., Elahi " )
assert rendered [ ai_index + 1 ] . startswith ( " The author(s) declare " )
def test_render_page_blocks_orders_references_within_column ( tmp_path : Path ) - > None :
from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" parsing_res_list " : [
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{
" block_id " : 1 ,
" block_label " : " paragraph_title " ,
" block_bbox " : [ 90 , 120 , 330 , 160 ] ,
" block_content " : " References " ,
} ,
{
" block_id " : 2 ,
" block_label " : " reference_content " ,
" block_bbox " : [ 620 , 200 , 1100 , 250 ] ,
" block_content " : " Bagnato, G. L. (2016). " ,
} ,
{
" block_id " : 3 ,
" block_label " : " reference_content " ,
" block_bbox " : [ 90 , 200 , 520 , 250 ] ,
" block_content " : " Amin, B. (2019). " ,
} ,
{
" block_id " : 4 ,
" block_label " : " reference_content " ,
" block_bbox " : [ 90 , 300 , 520 , 350 ] ,
" block_content " : " Cai, J. (2018). " ,
} ,
{
" block_id " : 5 ,
" block_label " : " reference_content " ,
" block_bbox " : [ 620 , 300 , 1100 , 350 ] ,
" block_content " : " Bentley, G. (2012). " ,
} ,
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] ,
} ,
" inputImage " : " " ,
}
rendered = render_page_blocks ( vault , 22 , result , images_dir , page_cache_dir , pdf_doc = None )
ref_items = [ line for line in rendered if line . startswith ( ( " Amin " , " Cai " , " Bagnato " , " Bentley " ) ) ]
assert ref_items == [ " Amin, B. (2019). " , " Cai, J. (2018). " , " Bagnato, G. L. (2016). " , " Bentley, G. (2012). " ]
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def test_render_page_blocks_keeps_top_figure_before_body_and_keeps_author_et_al_sentence_in_body (
tmp_path : Path ,
) - > None :
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from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
page_image = page_cache_dir / " page_008.png "
Image . new ( " RGB " , ( 1200 , 1600 ) , color = " white " ) . save ( page_image )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" parsing_res_list " : [
{
" block_id " : 1 ,
" block_label " : " figure_title " ,
" block_order " : 0 ,
" block_bbox " : [ 97 , 114 , 306 , 197 ] ,
" block_content " : " Fig. 3 Schematic representation of mechanical stimulation for tissue engineering constructs " ,
} ,
{
" block_id " : 2 ,
" block_label " : " image " ,
" block_order " : 1 ,
" block_bbox " : [ 374 , 117 , 1089 , 436 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 3 ,
" block_label " : " paragraph_title " ,
" block_order " : 2 ,
" block_bbox " : [ 96 , 470 , 513 , 520 ] ,
" block_content " : " 2.5 Electrical stimulation for tissue-engineered articular cartilage " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 3 ,
" block_bbox " : [ 95 , 543 , 583 , 918 ] ,
" block_content " : " As hyaline cartilage is an avascular tissue, the synovial fluid is responsible for chondrocyte nutrition and maintenance. " ,
} ,
{
" block_id " : 5 ,
" block_label " : " text " ,
" block_order " : 4 ,
" block_bbox " : [ 95 , 920 , 583 , 1043 ] ,
" block_content " : " Regenerative pathways for cartilage regeneration on iPSCs engineered constructs can be stimulated by endogenous electrical stimulation. " ,
} ,
{
" block_id " : 6 ,
" block_label " : " text " ,
" block_order " : 5 ,
" block_bbox " : [ 95 , 1045 , 583 , 1265 ] ,
" block_content " : " After incorporating ES on stem cells, this stimulus generates ATP oscillations driven by calcium oscillations. " ,
} ,
{
" block_id " : 7 ,
" block_label " : " paragraph_title " ,
" block_order " : 6 ,
" block_bbox " : [ 607 , 893 , 736 , 917 ] ,
" block_content " : " 3 Discussion " ,
} ,
{
" block_id " : 8 ,
" block_label " : " text " ,
" block_order " : 7 ,
" block_bbox " : [ 604 , 943 , 1094 , 1341 ] ,
" block_content " : " Bioreactors can be one of the most efficient and reliable methods for testing in vitro articular cartilage-engineered constructs. " ,
} ,
{
" block_id " : 9 ,
" block_label " : " text " ,
" block_order " : 8 ,
" block_bbox " : [ 95 , 1268 , 583 , 1418 ] ,
" block_content " : " Kwon et al. demonstrated that ES also drives ATP oscillations by cAMP modulation, leading to chondrogenic differentiation in the absence of exogenous growth factors. " ,
} ,
] ,
} ,
" inputImage " : " " ,
}
with patch ( " paperforge.worker.ocr.render_pdf_page_cached " , return_value = page_image ) :
rendered = render_page_blocks ( vault , 8 , result , images_dir , page_cache_dir , pdf_doc = None )
body_lines = [ line for line in rendered if line and not line . startswith ( " <!-- page " ) ]
assert body_lines [ 0 ] . startswith ( " Fig. 3 Schematic representation " )
assert body_lines [ 1 ] . startswith ( " ![[ " )
assert body_lines [ 2 ] == " ### 2.5 Electrical stimulation for tissue-engineered articular cartilage "
assert body_lines [ 6 ] . startswith ( " Kwon et al. demonstrated " )
assert body_lines [ 7 ] == " ### 3 Discussion "
def test_validate_block_order_preserves_full_width_blocks_between_columns ( ) - > None :
from paperforge . worker . ocr import validate_block_order
blocks = [
{
" block_id " : 1 ,
" block_label " : " abstract " ,
" block_order " : 6 ,
" block_bbox " : [ 96 , 603 , 1094 , 800 ] ,
" block_content " : " BACKGROUND " ,
} ,
{
" block_id " : 2 ,
" block_label " : " abstract " ,
" block_order " : 7 ,
" block_bbox " : [ 97 , 802 , 1094 , 851 ] ,
" block_content " : " METHODS " ,
} ,
{
" block_id " : 3 ,
" block_label " : " abstract " ,
" block_order " : 8 ,
" block_bbox " : [ 96 , 899 , 1093 , 977 ] ,
" block_content " : " CONCLUSION " ,
} ,
{
" block_id " : 4 ,
" block_label " : " text " ,
" block_order " : 9 ,
" block_bbox " : [ 97 , 1000 , 872 , 1025 ] ,
" block_content " : " Keywords " ,
} ,
{
" block_id " : 5 ,
" block_label " : " paragraph_title " ,
" block_order " : 10 ,
" block_bbox " : [ 98 , 1062 , 246 , 1086 ] ,
" block_content " : " 1 Introduction " ,
} ,
{
" block_id " : 6 ,
" block_label " : " text " ,
" block_order " : 11 ,
" block_bbox " : [ 96 , 1113 , 582 , 1190 ] ,
" block_content " : " Introduction body " ,
} ,
{
" block_id " : 7 ,
" block_label " : " text " ,
" block_order " : 12 ,
" block_bbox " : [ 604 , 1063 , 1094 , 1414 ] ,
" block_content " : " Right column body " ,
} ,
]
ordered = validate_block_order ( blocks , page_width = 1191 )
assert [ block [ " block_content " ] for block in ordered [ : 5 ] ] == [
" BACKGROUND " ,
" METHODS " ,
" CONCLUSION " ,
" Keywords " ,
" 1 Introduction " ,
]
def test_render_page_blocks_keeps_abstract_heading_before_abstract_body_on_first_page ( tmp_path : Path ) - > None :
from paperforge . worker . ocr import render_page_blocks
vault = tmp_path / " vault "
images_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " images "
page_cache_dir = vault / " System " / " PaperForge " / " ocr " / " KEY " / " pages "
images_dir . mkdir ( parents = True )
page_cache_dir . mkdir ( parents = True )
result = {
" prunedResult " : {
" width " : 1200 ,
" height " : 1600 ,
" parsing_res_list " : [
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{
" block_id " : 1 ,
" block_label " : " doc_title " ,
" block_order " : 0 ,
" block_bbox " : [ 96 , 210 , 949 , 284 ] ,
" block_content " : " Paper Title " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_order " : 1 ,
" block_bbox " : [ 95 , 312 , 761 , 365 ] ,
" block_content " : " Author One · Author Two " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_order " : 2 ,
" block_bbox " : [ 96 , 485 , 880 , 528 ] ,
" block_content " : " Received: 10 February 2023 " ,
} ,
{
" block_id " : 4 ,
" block_label " : " paragraph_title " ,
" block_order " : 3 ,
" block_bbox " : [ 97 , 577 , 181 , 599 ] ,
" block_content " : " Abstract " ,
} ,
{
" block_id " : 5 ,
" block_label " : " abstract " ,
" block_order " : 4 ,
" block_bbox " : [ 96 , 603 , 1094 , 800 ] ,
" block_content " : " BACKGROUND: Background text. " ,
} ,
{
" block_id " : 6 ,
" block_label " : " abstract " ,
" block_order " : 5 ,
" block_bbox " : [ 97 , 802 , 1094 , 851 ] ,
" block_content " : " METHODS: Methods text. " ,
} ,
{
" block_id " : 7 ,
" block_label " : " abstract " ,
" block_order " : 6 ,
" block_bbox " : [ 96 , 899 , 1093 , 977 ] ,
" block_content " : " CONCLUSION: Conclusion text. " ,
} ,
{
" block_id " : 8 ,
" block_label " : " text " ,
" block_order " : 7 ,
" block_bbox " : [ 97 , 1000 , 872 , 1025 ] ,
" block_content " : " Keywords one two three " ,
} ,
{
" block_id " : 9 ,
" block_label " : " paragraph_title " ,
" block_order " : 8 ,
" block_bbox " : [ 98 , 1062 , 246 , 1086 ] ,
" block_content " : " 1 Introduction " ,
} ,
{
" block_id " : 10 ,
" block_label " : " text " ,
" block_order " : 9 ,
" block_bbox " : [ 96 , 1113 , 582 , 1190 ] ,
" block_content " : " Introduction body. " ,
} ,
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] ,
} ,
" inputImage " : " " ,
}
rendered = render_page_blocks ( vault , 1 , result , images_dir , page_cache_dir , pdf_doc = None )
body_lines = [ line for line in rendered if line and not line . startswith ( " <!-- page " ) ]
abstract_idx = body_lines . index ( " ### Abstract " )
background_idx = body_lines . index ( " BACKGROUND: Background text. " )
methods_idx = body_lines . index ( " METHODS: Methods text. " )
conclusion_idx = body_lines . index ( " CONCLUSION: Conclusion text. " )
keywords_idx = body_lines . index ( " Keywords one two three " )
intro_idx = body_lines . index ( " ### 1 Introduction " )
assert abstract_idx < background_idx < methods_idx < conclusion_idx < keywords_idx < intro_idx
def test_media_clusters_merge_side_by_side_panels_with_small_gap ( ) - > None :
from paperforge . worker . ocr import media_clusters
blocks = [
{ " block_id " : 1 , " block_label " : " image " , " block_bbox " : [ 366 , 165 , 631 , 766 ] , " block_content " : " " } ,
{ " block_id " : 2 , " block_label " : " image " , " block_bbox " : [ 675 , 118 , 1091 , 738 ] , " block_content " : " " } ,
]
block_to_cluster , clusters = media_clusters ( blocks )
assert len ( clusters ) == 1
assert block_to_cluster [ 1 ] == block_to_cluster [ 2 ]
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def test_embedded_figure_text_excludes_body_paragraph_like_text ( ) - > None :
from paperforge . worker . ocr import is_embedded_figure_text_block
blocks = [
{
" block_id " : 1 ,
" block_label " : " paragraph_title " ,
" block_bbox " : [ 80 , 530 , 269 , 554 ] ,
" block_content " : " Immunohistochemistry " ,
} ,
{
" block_id " : 2 ,
" block_label " : " text " ,
" block_bbox " : [ 78 , 577 , 498 , 915 ] ,
" block_content " : (
" To determine which cells express these proteins, we performed immunohistochemical analyses "
" for Tyk2, S100A9, and ZNF 217 from the same tissues used in 2-DE. Positively stained cells "
" of Tyk2 and ZNF 217 were located at cytoplasm of epithelial cells. Although the majority of "
" cases of SCC and adjacent normal tissues showed cytoplasmic S100A9 positivity of epithelial "
" cells, some cases also showed nuclear S100A9 positivity, as shown in Fig. 3. "
) ,
} ,
{
" block_id " : 3 ,
" block_label " : " image " ,
" block_bbox " : [ 272 , 964 , 610 , 1421 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 4 ,
" block_label " : " image " ,
" block_bbox " : [ 620 , 964 , 933 , 1421 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 5 ,
" block_label " : " figure_title " ,
" block_bbox " : [ 78 , 1448 , 1129 , 1511 ] ,
" block_content " : (
" Fig. 3. Immunohistochemical staining in SCC and adjacent normal tissues. Sections from SCC and "
" nontumorous tissue were immunostained with antibodies against Tyk2 (left), S100A9 (middle), "
" and ZNF 217 (right). "
) ,
} ,
]
assert is_embedded_figure_text_block ( blocks [ 1 ] , blocks , page_width = 1200 , page_height = 1600 ) is False
def test_embedded_figure_text_keeps_narrow_in_figure_note ( ) - > None :
from paperforge . worker . ocr import is_embedded_figure_text_block
blocks = [
{
" block_id " : 1 ,
" block_label " : " chart " ,
" block_bbox " : [ 320 , 260 , 620 , 1080 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 2 ,
" block_label " : " chart " ,
" block_bbox " : [ 640 , 260 , 920 , 1080 ] ,
" block_content " : " " ,
} ,
{
" block_id " : 3 ,
" block_label " : " text " ,
" block_bbox " : [ 470 , 1090 , 760 , 1160 ] ,
" block_content " : " Patient A \n Age 42 \n HPV16 positive " ,
} ,
{
" block_id " : 4 ,
" block_label " : " figure_title " ,
" block_bbox " : [ 300 , 1180 , 980 , 1250 ] ,
" block_content " : " Figure 2. Representative pathology records and imaging findings. " ,
} ,
]
assert is_embedded_figure_text_block ( blocks [ 2 ] , blocks , page_width = 1200 , page_height = 1600 ) is True
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# --- Structured renderer regression tests ---
def test_structured_renderer_abstract_before_introduction ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" role " : " section_heading " ,
" text " : " 1 Introduction " ,
" render_default " : True ,
" page " : 1 ,
} ,
{
" role " : " abstract_heading " ,
" text " : " " ,
" render_default " : True ,
" page " : 1 ,
} ,
{
" role " : " abstract_body " ,
" text " : " This is the abstract body text. " ,
" render_default " : True ,
" page " : 1 ,
} ,
{
" role " : " body_paragraph " ,
" text " : " Some body paragraph after the introduction heading. " ,
" render_default " : True ,
" page " : 1 ,
} ,
]
output = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
abstract_idx = output . index ( " ## Abstract " )
abstract_text_idx = output . index ( " This is the abstract body text. " )
intro_idx = output . index ( " ## 1 Introduction " )
assert abstract_idx < abstract_text_idx < intro_idx
def test_structured_renderer_figure_and_table_links_rendered ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" role " : " figure_caption " ,
" text " : " Figure 1. A test figure caption. " ,
" render_default " : True ,
" page " : 1 ,
} ,
{
" role " : " table_caption " ,
" text " : " Table 1. A test table caption. " ,
" render_default " : True ,
" page " : 1 ,
} ,
{
" role " : " body_paragraph " ,
" text " : " Body text between figures and tables. " ,
" render_default " : True ,
" page " : 1 ,
} ,
]
figure_inventory = {
" matched_figures " : [
{ " figure_id " : " fig_001 " } ,
]
}
table_inventory = {
" tables " : [
{ " table_id " : " tbl_001 " , " has_asset " : True } ,
]
}
output = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = figure_inventory ,
table_inventory = table_inventory ,
)
assert " ![[render/figures/fig_001.md]] " in output
assert " ![[render/tables/tbl_001.md]] " in output
def test_structured_renderer_respects_render_default_false ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" role " : " body_paragraph " ,
" text " : " VISIBLE_BODY " ,
" render_default " : True ,
" page " : 1 ,
} ,
{
" role " : " body_paragraph " ,
" text " : " HIDDEN_BODY " ,
" render_default " : False ,
" page " : 1 ,
} ,
{
" role " : " section_heading " ,
" text " : " Hidden Heading " ,
" render_default " : False ,
" page " : 2 ,
} ,
{
" role " : " body_paragraph " ,
" text " : " ALSO_VISIBLE " ,
" render_default " : True ,
" page " : 2 ,
} ,
]
output = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " VISIBLE_BODY " in output
assert " ALSO_VISIBLE " in output
assert " HIDDEN_BODY " not in output
assert " Hidden Heading " not in output
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def test_stabilize_renderer_output_starts_with_title ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
md = render_fulltext_markdown (
structured_blocks = [
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{
" paper_id " : " KEY001 " ,
" page " : 1 ,
" block_id " : " b1 " ,
" role " : " body_paragraph " ,
" text " : " Body. " ,
" render_default " : True ,
} ,
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] ,
resolved_metadata = { " title " : { " value " : " The Paper Title " } } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert md . startswith ( " # The Paper Title " )
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def test_structured_renderer_no_duplicate_authors ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 1 ,
" block_id " : " b1 " ,
" role " : " authors " ,
" text " : " Alice Smith, Bob Jones " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 1 ,
" block_id " : " b2 " ,
" role " : " abstract_heading " ,
" text " : " Abstract " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 1 ,
" block_id " : " b3 " ,
" role " : " abstract_body " ,
" text " : " Abstract body text. " ,
" render_default " : True ,
} ,
]
resolved_metadata = {
" title " : { " value " : " Test Paper " } ,
" authors " : { " value " : [ " Alice Smith " , " Bob Jones " ] } ,
" journal " : { " value " : " Test Journal " } ,
" year " : { " value " : 2025 } ,
" doi " : { " value " : " 10.1000/xyz " } ,
}
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = resolved_metadata ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert md . count ( " Alice Smith " ) == 1
assert md . count ( " Bob Jones " ) == 1
def test_structured_renderer_no_inline_table_html ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 1 ,
" block_id " : " b1 " ,
" role " : " body_paragraph " ,
" text " : " The results are shown below: \n <table><tr><td>Tabular data</td></tr></table> " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 1 ,
" block_id " : " b2 " ,
" role " : " body_paragraph " ,
" text " : " Body text after table. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " <table> " not in md
def test_structured_renderer_backmatter_sections ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 3 ,
" block_id " : " b1 " ,
" role " : " backmatter_heading " ,
" text " : " Author contributions " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 3 ,
" block_id " : " b2 " ,
" role " : " backmatter_body " ,
" text " : " AS and BJ designed the study. CJ collected the data. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 3 ,
" block_id " : " b3 " ,
" role " : " backmatter_heading " ,
" text " : " Funding " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 3 ,
" block_id " : " b4 " ,
" role " : " backmatter_body " ,
" text " : " This work was supported by NIH grant R01-XX. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " ## Author contributions " in md
assert " AS and BJ designed the study " in md
assert " ## Funding " in md
def test_structured_renderer_references_as_heading ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b1 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b2 " ,
" role " : " reference_item " ,
" text " : " Smith J, Jones B. (2024) A study on something. Journal of Examples. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " ## References " in md
def test_structured_renderer_heading_body_attachment ( ) - > None :
""" Headings with interleaved bodies attach correctly, not cross-wired. """
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b1 " ,
" role " : " backmatter_heading " ,
" text " : " Generative AI statement " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b2 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b3 " ,
" role " : " backmatter_heading " ,
" text " : " Publisher ' s note " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b4 " ,
" role " : " backmatter_body " ,
" text " : " The authors declare no AI-generated content. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b5 " ,
" role " : " backmatter_body " ,
" text " : " Springer Nature remains neutral. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b6 " ,
" role " : " reference_item " ,
" text " : " Smith J. (2024) A study. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b7 " ,
" role " : " reference_item " ,
" text " : " Jones B. (2023) Another study. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " ## Generative AI statement " in md
assert " ## References " in md
assert " ## Publisher ' s note " in md
gen_ai_idx = md . index ( " ## Generative AI statement " )
refs_idx = md . index ( " ## References " )
pub_idx = md . index ( " ## Publisher ' s note " )
decl_idx = md . index ( " The authors declare no AI-generated content. " )
springer_idx = md . index ( " Springer Nature remains neutral. " )
smith_idx = md . index ( " Smith J. (2024) A study. " )
jones_idx = md . index ( " Jones B. (2023) Another study. " )
assert gen_ai_idx < decl_idx , " Generative AI body should appear after its heading "
assert decl_idx < pub_idx , " Generative AI body should appear before Publisher ' s note "
assert pub_idx < springer_idx , " Publisher ' s note body should appear after its heading "
assert refs_idx > springer_idx , " References should appear after all backmatter sections "
assert smith_idx > refs_idx and jones_idx > refs_idx , " Reference items should appear under References "
def test_structured_renderer_mixed_column_ordering ( ) - > None :
""" Two-column tail page blocks resolve to correct heading-body attachment. """
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b1 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b2 " ,
" role " : " backmatter_heading " ,
" text " : " Generative AI statement " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b3 " ,
" role " : " backmatter_heading " ,
" text " : " Publisher ' s note " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b4 " ,
" role " : " reference_item " ,
" text " : " Smith J. (2024) A study. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b5 " ,
" role " : " reference_item " ,
" text " : " Jones B. (2023) Another study. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b6 " ,
" role " : " backmatter_body " ,
" text " : " The authors declare no AI-generated content. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b7 " ,
" role " : " backmatter_body " ,
" text " : " Springer Nature remains neutral. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b8 " ,
" role " : " backmatter_heading " ,
" text " : " Supplementary material " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b9 " ,
" role " : " backmatter_body " ,
" text " : " Supplementary data are available online. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
gen_ai_idx = md . index ( " ## Generative AI statement " )
refs_idx = md . index ( " ## References " )
pub_idx = md . index ( " ## Publisher ' s note " )
supp_idx = md . index ( " ## Supplementary material " )
decl_idx = md . index ( " The authors declare no AI-generated content. " )
springer_idx = md . index ( " Springer Nature remains neutral. " )
smith_idx = md . index ( " Smith J. (2024) A study. " )
assert gen_ai_idx < decl_idx , " Generative AI body after its heading "
assert decl_idx < pub_idx , " Generative AI body before Publisher ' s note "
assert pub_idx < springer_idx , " Publisher ' s note body after its heading "
assert springer_idx < supp_idx , " Supplementary material after Publisher ' s note "
assert refs_idx > supp_idx , " References should appear after all backmatter sections "
assert smith_idx > refs_idx , " Reference items should appear under References "
assert md . index ( " Supplementary data are available online. " ) > supp_idx , (
" Supplementary body under Supplementary heading "
)
def test_tail_zone_noise_band_guard ( ) - > None :
""" Mixed tail page: backmatter body in left column below ref items gets stolen.
Block order simulates a real OCR scan where a backmatter_body block
lands in the left column ( from a left - column backmatter heading like
" Author contributions " ) , interleaved AFTER reference_items in column - sorted
order . The FIFO heading_queue has no heading to match it , so ref_section
absorbs it incorrectly .
"""
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b1 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
" block_bbox " : [ 80 , 100 , 520 , 140 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b2 " ,
" role " : " reference_item " ,
" text " : " Smith J. (2024) A study on electric fields. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 180 , 520 , 220 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b3 " ,
" role " : " reference_item " ,
" text " : " Jones B. (2023) Another study on galvanotaxis. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 260 , 520 , 300 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b4 " ,
" role " : " backmatter_body " ,
" text " : " AS and BJ designed the study. CJ collected the data. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 340 , 520 , 380 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b5 " ,
" role " : " backmatter_heading " ,
" text " : " Author contributions " ,
" render_default " : True ,
" block_bbox " : [ 620 , 50 , 1100 , 90 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b6 " ,
" role " : " backmatter_heading " ,
" text " : " Generative AI statement " ,
" render_default " : True ,
" block_bbox " : [ 620 , 400 , 1100 , 440 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b7 " ,
" role " : " backmatter_body " ,
" text " : " The authors declare no AI-generated content. " ,
" render_default " : True ,
" block_bbox " : [ 620 , 480 , 1100 , 520 ] ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " ## Author contributions " in md
assert " ## References " in md
assert " ## Generative AI statement " in md
gen_ai_idx = md . index ( " ## Generative AI statement " )
refs_idx = md . index ( " ## References " )
decl_idx = md . index ( " The authors declare no AI-generated content. " )
contributions_idx = md . index ( " AS and BJ designed the study " )
assert contributions_idx < refs_idx , (
" Author contributions body should appear BEFORE References, not absorbed into ref_section "
)
assert gen_ai_idx < decl_idx < refs_idx , " Gen AI section (heading + body) before References, body after its heading "
def test_tail_zone_supplementary_material_not_noise ( ) - > None :
""" Supplementary material body in usable middle band is not treated as noise. """
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b1 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
" block_bbox " : [ 80 , 450 , 520 , 490 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b2 " ,
" role " : " reference_item " ,
" text " : " Smith J. (2024) A study. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 520 , 520 , 560 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b3 " ,
" role " : " backmatter_heading " ,
" text " : " Supplementary material " ,
" render_default " : True ,
" block_bbox " : [ 620 , 120 , 1100 , 160 ] ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b4 " ,
" role " : " backmatter_body " ,
" text " : " Supplementary material body in the middle band of the page. " ,
" render_default " : True ,
" block_bbox " : [ 620 , 300 , 1100 , 350 ] ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
assert " ## Supplementary material " in md
assert " Supplementary material body in the middle band " in md
def test_tail_candidate_overreach_does_not_absorb_late_body ( ) - > None :
""" Late body paragraphs are NOT absorbed into backmatter sections.
The FIFO fallback in _reorder_tail_run_fifo treats body_paragraph as
attachable to the heading_queue , causing late body text to be pulled
into the backmatter section instead of appearing before it .
"""
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b1 " ,
" role " : " body_paragraph " ,
" text " : " In conclusion, this study demonstrates that the proposed approach achieves significant improvement across all evaluated metrics, outperforming existing methods in both accuracy and efficiency. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b2 " ,
" role " : " body_paragraph " ,
" text " : " Future work should investigate the applicability of this framework to larger patient cohorts and broader clinical contexts. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b3 " ,
" role " : " backmatter_heading " ,
" text " : " Funding " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b4 " ,
" role " : " backmatter_body " ,
" text " : " This work was supported by NIH grant R01-XX and NSF grant DMR-1234. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
body_idx = md . index ( " In conclusion, this study demonstrates " )
funding_idx = md . index ( " ## Funding " )
assert body_idx < funding_idx , (
" Late body paragraphs should appear before backmatter sections, not absorbed into them "
)
def test_cross_page_funding_continuation_preserves_order ( ) - > None :
""" Funding body continuation on next page stays before References.
Cross - page continuation of a backmatter body ( tail_candidate_body on
a subsequent page ) should be placed after its heading and before any
References section . Current FIFO fallback absorbs it into the
reference zone when reference_heading precedes it .
"""
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b1 " ,
" role " : " backmatter_heading " ,
" text " : " Funding " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 5 ,
" block_id " : " b2 " ,
" role " : " backmatter_body " ,
" text " : " This work was supported by NIH grant R01-XX. Additional funding was provided by NSF grant DMR-1234. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 6 ,
" block_id " : " b3 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 6 ,
" block_id " : " b4 " ,
" role " : " tail_candidate_body " ,
" text " : " The funders had no role in study design, data collection, analysis, decision to publish, or preparation of the manuscript. " ,
" render_default " : True ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 6 ,
" block_id " : " b5 " ,
" role " : " reference_item " ,
" text " : " Smith J, Jones B. (2024) A study on electric fields. Journal of Bioelectricity. " ,
" render_default " : True ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
)
funding_idx = md . index ( " ## Funding " )
continuation_idx = md . index ( " The funders had no role " )
refs_idx = md . index ( " ## References " )
assert funding_idx < continuation_idx , " Funding continuation should appear after its heading "
assert continuation_idx < refs_idx , (
" Funding continuation should appear before References, not absorbed into the reference section "
)
def test_mixed_tail_page_keeps_late_body_out_of_funding_and_attaches_real_funding ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 21 ,
" block_id " : " b1 " ,
" role " : " body_paragraph " ,
" text " : " Late conclusion paragraph that should stay in the main body before any tail sections. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 240 , 520 , 360 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 21 ,
" block_id " : " b2 " ,
" role " : " backmatter_heading " ,
" text " : " Funding " ,
" render_default " : True ,
" block_bbox " : [ 650 , 1200 , 900 , 1240 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 21 ,
" block_id " : " b3 " ,
" role " : " body_paragraph " ,
" text " : " This work was supported by Grant A and Grant B. " ,
" render_default " : True ,
" block_bbox " : [ 650 , 1280 , 1120 , 1500 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b4 " ,
" role " : " body_paragraph " ,
" text " : " Additional funding continuation text from the next page. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 160 , 520 , 320 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b5 " ,
" role " : " backmatter_heading " ,
" text " : " Acknowledgments " ,
" render_default " : True ,
" block_bbox " : [ 80 , 420 , 420 , 460 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b6 " ,
" role " : " backmatter_body " ,
" text " : " We thank our collaborators. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 500 , 520 , 620 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b7 " ,
" role " : " reference_heading " ,
" text " : " References " ,
" render_default " : True ,
" block_bbox " : [ 80 , 700 , 320 , 740 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 22 ,
" block_id " : " b8 " ,
" role " : " reference_item " ,
" text " : " Smith J. (2024) Tail ordering paper. " ,
" render_default " : True ,
" block_bbox " : [ 80 , 780 , 520 , 840 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
page_count = 22 ,
)
late_body_idx = md . index ( " Late conclusion paragraph that should stay " )
funding_idx = md . index ( " ## Funding " )
funding_body_idx = md . index ( " This work was supported by Grant A " )
funding_cont_idx = md . index ( " Additional funding continuation text " )
ack_idx = md . index ( " ## Acknowledgments " )
refs_idx = md . index ( " ## References " )
assert late_body_idx < funding_idx , " Late body text must remain before Funding "
assert funding_idx < funding_body_idx < funding_cont_idx , " Funding body and continuation must stay under Funding "
assert funding_cont_idx < ack_idx < refs_idx , " Funding continuation must complete before later tail sections "
2026-06-05 16:46:49 +00:00
def test_backmatter_boundary_normalizes_child_sections_before_references ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
structured_blocks = [
{
" paper_id " : " KEY001 " ,
" page " : 10 ,
" block_id " : " b1 " ,
" role " : " backmatter_boundary_heading " ,
" text " : " ADDITIONAL INFORMATION AND DECLARATIONS " ,
" render_default " : True ,
" block_bbox " : [ 360 , 1200 , 1080 , 1240 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 10 ,
" block_id " : " b2 " ,
" role " : " backmatter_heading " ,
" text " : " Funding " ,
" render_default " : True ,
" block_bbox " : [ 360 , 1280 , 520 , 1320 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 10 ,
" block_id " : " b3 " ,
" role " : " backmatter_body " ,
" text " : " The work was supported by Grant A. " ,
" render_default " : True ,
" block_bbox " : [ 360 , 1330 , 1120 , 1450 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b4 " ,
" role " : " subsection_heading " ,
" text " : " Grant Disclosures " ,
" render_default " : True ,
" block_bbox " : [ 360 , 160 , 620 , 200 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b5 " ,
" role " : " body_paragraph " ,
" text " : " Grant A was disclosed by the authors. " ,
" render_default " : True ,
" block_bbox " : [ 360 , 210 , 920 , 290 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b6 " ,
" role " : " backmatter_heading " ,
" text " : " Author Contributions " ,
" render_default " : True ,
" block_bbox " : [ 360 , 320 , 720 , 360 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b7 " ,
" role " : " frontmatter_noise " ,
" text " : " Author A conceived the study and wrote the manuscript. " ,
" render_default " : True ,
" block_bbox " : [ 360 , 370 , 1120 , 430 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b8 " ,
" role " : " backmatter_heading " ,
" text " : " Data Availability " ,
" render_default " : True ,
" block_bbox " : [ 360 , 460 , 680 , 500 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b9 " ,
" role " : " body_paragraph " ,
" text " : " The raw data has been supplied as Supplementary Files. " ,
" render_default " : True ,
" block_bbox " : [ 360 , 510 , 980 , 560 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b10 " ,
" role " : " backmatter_boundary_heading " ,
" text " : " Supplemental Information " ,
" render_default " : True ,
" block_bbox " : [ 360 , 590 , 760 , 630 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b11 " ,
" role " : " body_paragraph " ,
" text " : " Supplemental information for this article can be found online. " ,
" render_default " : True ,
" block_bbox " : [ 360 , 640 , 1120 , 700 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b12 " ,
" role " : " reference_heading " ,
" text " : " REFERENCES " ,
" render_default " : True ,
" block_bbox " : [ 360 , 760 , 620 , 800 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
{
" paper_id " : " KEY001 " ,
" page " : 11 ,
" block_id " : " b13 " ,
" role " : " reference_item " ,
" text " : " Smith J. Example reference. " ,
" render_default " : True ,
" block_bbox " : [ 360 , 820 , 1000 , 880 ] ,
" page_width " : 1200 ,
" page_height " : 1700 ,
} ,
]
md = render_fulltext_markdown (
structured_blocks = structured_blocks ,
resolved_metadata = { } ,
figure_inventory = { } ,
table_inventory = { } ,
page_count = 11 ,
)
funding_idx = md . index ( " ## Funding " )
grant_idx = md . index ( " ## Grant Disclosures " )
author_idx = md . index ( " ## Author Contributions " )
data_idx = md . index ( " ## Data Availability " )
supp_idx = md . index ( " ## Supplemental Information " )
refs_idx = md . index ( " ## REFERENCES " )
grant_body_idx = md . index ( " Grant A was disclosed by the authors. " )
author_body_idx = md . index ( " Author A conceived the study " )
data_body_idx = md . index ( " The raw data has been supplied " )
supp_body_idx = md . index ( " Supplemental information for this article " )
assert funding_idx < grant_idx < author_idx < data_idx < supp_idx < refs_idx
assert grant_idx < grant_body_idx < author_idx
assert author_idx < author_body_idx < data_idx
assert data_idx < data_body_idx < supp_idx
assert supp_idx < supp_body_idx < refs_idx
2026-06-06 02:08:42 +00:00
def test_unresolved_cluster_appears_in_fulltext ( ) - > None :
from paperforge . worker . ocr_render import render_fulltext_markdown
md = render_fulltext_markdown (
structured_blocks = [
{
" role " : " body_paragraph " ,
" text " : " Body text on page 1. " ,
" render_default " : True ,
" page " : 1 ,
} ,
] ,
resolved_metadata = { } ,
figure_inventory = {
" unresolved_clusters " : [
{
" cluster_id " : " cluster_001 " ,
" page " : 1 ,
" bbox " : [ 0 , 0 , 100 , 100 ] ,
" media_block_ids " : [ 1 , 2 ] ,
" status " : " unresolved_multi_panel " ,
" confidence " : 0.45 ,
}
]
} ,
table_inventory = { } ,
)
assert " ![[render/figures/cluster_001.md]] " in md
