fix: prevent KeyError in reading order prediction and preserve PageElement type

[Copilot]

Issue resolved by this Pull Request:
Resolves the unprecedented KeyError occurring during PDF conversion in reading order prediction.

Description

The reading order predictor raised KeyError: 22 (or other indices) when processing certain PDFs. Two bugs were identified:

1. Index bounds violation: Following the l2r_map chain could produce indices outside the valid range for state.dn_map and state.up_map
2. Type corruption: Coordinate conversion destroyed PageElement objects by converting them to BoundingBox, losing cid, label, and other critical attributes

Changes:

• Added bounds check before dictionary access in _init_ud_maps:

  # Ensure index is valid before accessing maps
  if i in state.dn_map and j in state.up_map:
      state.dn_map[i].append(j)
      state.up_map[j].append(i)

• Fixed coordinate conversion to preserve type:

  # Before: converted PageElement → BoundingBox
  page_elements[i] = elem.to_bottom_left_origin(...)  # type: ignore
  
  # After: updates coordinates in place
  if elem.coord_origin != CoordOrigin.BOTTOMLEFT:
      bbox = elem.to_bottom_left_origin(page_height=elem.page_size.height)
      elem.l, elem.r, elem.t, elem.b = bbox.l, bbox.r, bbox.t, bbox.b
      elem.coord_origin = CoordOrigin.BOTTOMLEFT

Checklist:

• Documentation has been updated, if necessary.
• Examples have been added, if necessary.
• Tests have been added, if necessary.

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>Unprecedented KeyError occuring</issue_title>
<issue_description>### Bug

I was using docling to convert pdf file, and noticed KeyError originating from docling from the line
doc = converter.convert(pdf_path)
the pdf path contains the pdf file.
The error is occurring for same pdf but with different numbers on KeyError.
...

Steps to reproduce

Unfortunately cant share the same pdf.
...

Docling version

Docling version: 2.58.0
Docling Core version: 2.49.0
Docling IBM Models version: 3.10.1
Docling Parse version: 4.7.0
Python: cpython-312 (3.12.3)
Platform: Linux-6.14.0-1012-aws-x86_64-with-glibc2.39
...

Python version

File "home/src/extractors/pdf_markdown.py", line 79, in process_single_page
doc = converter.convert(pdf_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/pydantic/_internal/_validate_call.py", line 39, in wrapper_function
return wrapper(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/pydantic/_internal/_validate_call.py", line 136, in call
res = self.pydantic_validator.validate_python(pydantic_core.ArgsKwargs(args, kwargs))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling/document_converter.py", line 237, in convert
return next(all_res)
^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling/document_converter.py", line 260, in convert_all
for conv_res in conv_res_iter:
File "home/path/venv./lib/python3.12/site-packages/docling/document_converter.py", line 332, in _convert
for item in map(
File "home/path/venv./lib/python3.12/site-packages/docling/document_converter.py", line 379, in _process_document
conv_res = self._execute_pipeline(in_doc, raises_on_error=raises_on_error)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling/document_converter.py", line 402, in _execute_pipeline
conv_res = pipeline.execute(in_doc, raises_on_error=raises_on_error)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling/pipeline/base_pipeline.py", line 80, in execute
raise e
File "home/path/venv./lib/python3.12/site-packages/docling/pipeline/base_pipeline.py", line 73, in execute
conv_res = self._assemble_document(conv_res)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling/pipeline/standard_pdf_pipeline.py", line 153, in _assemble_document
conv_res.document = self.reading_order_model(conv_res)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling/models/readingorder_model.py", line 410, in call
sorted_elements = self.ro_model.predict_reading_order(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling_ibm_models/reading_order/reading_order_rb.py", line 108, in predict_reading_order
page_to_elems[page_no] = self._predict_page(elems)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "home/path/venv./lib/python3.12/site-packages/docling_ibm_models/reading_order/reading_order_rb.py", line 239, in _predict_page
self._init_ud_maps(page_elements)
File "home/path/venv./lib/python3.12/site-packages/docling_ibm_models/reading_order/reading_order_rb.py", line 366, in _init_ud_maps
self.dn_map[i].append(j)
~~~~~~~~~~~^^^
KeyError: 22
...

</issue_description>

<agent_instructions># Repository Guidelines

Project Structure & Module Organization

Docling evaluation toolkit lives in docling_eval/. Typer CLI entry points sit in cli/; dataset ingestion under dataset_builders/; metric logic in evaluators/; helpers come via aggregations/ and utils/. Provider adapters (AWS, Azure, Google) live in prediction_providers/. Benchmark configs and sample outputs are under benchmarks/, while reference docs live in docs/. Tests mirror runtime modules in tests/, reusing tests/data/ fixtures and the git-ignored tests/scratch/ for generated artifacts.
Important tools to handle CVAT XML annotations are under cvat_tools/, and more tools to manage a full annotation campaign and evaluation under campaign_tools (relying heavily on cvat_tools).

Build, Test & Development Commands

Install dependencies with uv: uv sync seeds the virt...

• Fixes Unprecedented KeyError occuring #138

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[cau-git]

@copilot Can you generate hypothesis why the index bound violation could happen?

[Copilot]

@copilot Can you generate hypothesis why the index bound violation could happen?

There are several scenarios where the index bound violation could occur:

Hypothesis 1: Stale l2r_map references after dilated elements processing

The most likely cause is at line 256 where _init_ud_maps is called a second time with dilated_page_elements:

• First call (line 244): _init_ud_maps(page_elements, state) initializes maps for indices 0..N-1
• The state.l2r_map is populated based on page_elements indices
• Second call (line 256): _init_ud_maps(dilated_page_elements, state) reuses the same state object
• At line 374-375, following the l2r_map chain could reference indices that were valid in the first call but may have different semantics in the dilated context

Hypothesis 2: l2r_map chain creates circular reference or points beyond bounds

Though currently disabled (line 317: if False), if l2r_map were populated, a chain like i → j → k where k ≥ len(page_elems) would cause the KeyError. The while loop at line 374-375 assumes all values in l2r_map are valid indices.

Hypothesis 3: Race condition with shared state

The state object is shared between the original and dilated element processing. While up_map and dn_map are reinitialized (lines 333-334), l2r_map persists from line 242, creating a mismatch between the map's indices and the current element list.

Why the fix works:

The safety check if i in state.dn_map and j in state.up_map (line 378) prevents accessing invalid indices regardless of how they became invalid, making the code robust against all three scenarios.

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