94d0729c50
* Fix for md hanging when encountering long sequence of unescaped underscore chars Signed-off-by: Maksym Lysak <mly@zurich.ibm.com> * Added comment explaining reason for fix Signed-off-by: Maksym Lysak <mly@zurich.ibm.com> * Fixed trailing inline text handling (at the end of a file), and corrected underscore sequence shortening Signed-off-by: Maksym Lysak <mly@zurich.ibm.com> * making fix more rare Signed-off-by: Maksym Lysak <mly@zurich.ibm.com> --------- Signed-off-by: Maksym Lysak <mly@zurich.ibm.com> Co-authored-by: Maksym Lysak <mly@zurich.ibm.com>
347 lines
14 KiB
Python
347 lines
14 KiB
Python
import logging
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import re
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import warnings
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from io import BytesIO
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from pathlib import Path
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from typing import Set, Union
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import marko
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import marko.ext
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import marko.ext.gfm
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import marko.inline
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from docling_core.types.doc import (
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DocItemLabel,
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DoclingDocument,
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DocumentOrigin,
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GroupLabel,
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TableCell,
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TableData,
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)
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from marko import Markdown
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from docling.backend.abstract_backend import DeclarativeDocumentBackend
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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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_log = logging.getLogger(__name__)
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class MarkdownDocumentBackend(DeclarativeDocumentBackend):
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def shorten_underscore_sequences(self, markdown_text, max_length=10):
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# This regex will match any sequence of underscores
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pattern = r"_+"
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def replace_match(match):
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underscore_sequence = match.group(
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0
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) # Get the full match (sequence of underscores)
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# Shorten the sequence if it exceeds max_length
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if len(underscore_sequence) > max_length:
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return "_" * max_length
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else:
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return underscore_sequence # Leave it unchanged if it is shorter or equal to max_length
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# Use re.sub to replace long underscore sequences
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shortened_text = re.sub(pattern, replace_match, markdown_text)
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if len(shortened_text) != len(markdown_text):
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warnings.warn("Detected potentially incorrect Markdown, correcting...")
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return shortened_text
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def __init__(self, in_doc: "InputDocument", path_or_stream: Union[BytesIO, Path]):
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super().__init__(in_doc, path_or_stream)
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_log.debug("MD INIT!!!")
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# Markdown file:
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self.path_or_stream = path_or_stream
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self.valid = True
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self.markdown = "" # To store original Markdown string
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self.in_table = False
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self.md_table_buffer: list[str] = []
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self.inline_text_buffer = ""
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try:
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if isinstance(self.path_or_stream, BytesIO):
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text_stream = self.path_or_stream.getvalue().decode("utf-8")
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# remove invalid sequences
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# very long sequences of underscores will lead to unnecessary long processing times.
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# In any proper Markdown files, underscores have to be escaped,
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# otherwise they represent emphasis (bold or italic)
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self.markdown = self.shorten_underscore_sequences(text_stream)
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if isinstance(self.path_or_stream, Path):
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with open(self.path_or_stream, "r", encoding="utf-8") as f:
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md_content = f.read()
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# remove invalid sequences
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# very long sequences of underscores will lead to unnecessary long processing times.
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# In any proper Markdown files, underscores have to be escaped,
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# otherwise they represent emphasis (bold or italic)
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self.markdown = self.shorten_underscore_sequences(md_content)
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self.valid = True
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_log.debug(self.markdown)
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except Exception as e:
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raise RuntimeError(
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f"Could not initialize MD backend for file with hash {self.document_hash}."
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) from e
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return
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def close_table(self, doc=None):
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if self.in_table:
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_log.debug("=== TABLE START ===")
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for md_table_row in self.md_table_buffer:
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_log.debug(md_table_row)
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_log.debug("=== TABLE END ===")
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tcells = []
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result_table = []
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for n, md_table_row in enumerate(self.md_table_buffer):
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data = []
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if n == 0:
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header = [t.strip() for t in md_table_row.split("|")[1:-1]]
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for value in header:
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data.append(value)
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result_table.append(data)
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if n > 1:
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values = [t.strip() for t in md_table_row.split("|")[1:-1]]
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for value in values:
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data.append(value)
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result_table.append(data)
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for trow_ind, trow in enumerate(result_table):
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for tcol_ind, cellval in enumerate(trow):
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row_span = (
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1 # currently supporting just simple tables (without spans)
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)
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col_span = (
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1 # currently supporting just simple tables (without spans)
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)
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icell = TableCell(
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text=cellval.strip(),
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row_span=row_span,
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col_span=col_span,
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start_row_offset_idx=trow_ind,
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end_row_offset_idx=trow_ind + row_span,
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start_col_offset_idx=tcol_ind,
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end_col_offset_idx=tcol_ind + col_span,
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col_header=False,
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row_header=False,
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)
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tcells.append(icell)
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num_rows = len(result_table)
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num_cols = len(result_table[0])
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self.in_table = False
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self.md_table_buffer = [] # clean table markdown buffer
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# Initialize Docling TableData
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data = TableData(num_rows=num_rows, num_cols=num_cols, table_cells=tcells)
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# Populate
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for tcell in tcells:
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data.table_cells.append(tcell)
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if len(tcells) > 0:
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doc.add_table(data=data)
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return
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def process_inline_text(self, parent_element, doc=None):
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# self.inline_text_buffer += str(text_in)
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txt = self.inline_text_buffer.strip()
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if len(txt) > 0:
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doc.add_text(
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label=DocItemLabel.PARAGRAPH,
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parent=parent_element,
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text=txt,
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)
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self.inline_text_buffer = ""
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def iterate_elements(self, element, depth=0, doc=None, parent_element=None):
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# Iterates over all elements in the AST
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# Check for different element types and process relevant details
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if isinstance(element, marko.block.Heading):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(
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f" - Heading level {element.level}, content: {element.children[0].children}"
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)
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if element.level == 1:
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doc_label = DocItemLabel.TITLE
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else:
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doc_label = DocItemLabel.SECTION_HEADER
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# Header could have arbitrary inclusion of bold, italic or emphasis,
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# hence we need to traverse the tree to get full text of a header
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strings = []
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# Define a recursive function to traverse the tree
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def traverse(node):
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# Check if the node has a "children" attribute
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if hasattr(node, "children"):
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# If "children" is a list, continue traversal
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if isinstance(node.children, list):
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for child in node.children:
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traverse(child)
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# If "children" is text, add it to header text
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elif isinstance(node.children, str):
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strings.append(node.children)
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traverse(element)
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snippet_text = "".join(strings)
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if len(snippet_text) > 0:
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parent_element = doc.add_text(
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label=doc_label, parent=parent_element, text=snippet_text
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)
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elif isinstance(element, marko.block.List):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(f" - List {'ordered' if element.ordered else 'unordered'}")
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list_label = GroupLabel.LIST
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if element.ordered:
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list_label = GroupLabel.ORDERED_LIST
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parent_element = doc.add_group(
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label=list_label, name=f"list", parent=parent_element
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)
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elif isinstance(element, marko.block.ListItem):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(" - List item")
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snippet_text = str(element.children[0].children[0].children)
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is_numbered = False
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if parent_element.label == GroupLabel.ORDERED_LIST:
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is_numbered = True
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doc.add_list_item(
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enumerated=is_numbered, parent=parent_element, text=snippet_text
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)
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elif isinstance(element, marko.inline.Image):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(f" - Image with alt: {element.title}, url: {element.dest}")
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doc.add_picture(parent=parent_element, caption=element.title)
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elif isinstance(element, marko.block.Paragraph):
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self.process_inline_text(parent_element, doc)
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elif isinstance(element, marko.inline.RawText):
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_log.debug(f" - Paragraph (raw text): {element.children}")
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snippet_text = str(element.children).strip()
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# Detect start of the table:
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if "|" in snippet_text:
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# most likely part of the markdown table
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self.in_table = True
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if len(self.md_table_buffer) > 0:
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self.md_table_buffer[len(self.md_table_buffer) - 1] += str(
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snippet_text
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)
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else:
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self.md_table_buffer.append(snippet_text)
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else:
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self.close_table(doc)
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self.in_table = False
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# most likely just inline text
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self.inline_text_buffer += str(
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element.children
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) # do not strip an inline text, as it may contain important spaces
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elif isinstance(element, marko.inline.CodeSpan):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(f" - Code Span: {element.children}")
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snippet_text = str(element.children).strip()
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doc.add_text(
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label=DocItemLabel.CODE, parent=parent_element, text=snippet_text
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)
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elif isinstance(element, marko.block.CodeBlock):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(f" - Code Block: {element.children}")
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snippet_text = str(element.children[0].children).strip()
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doc.add_text(
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label=DocItemLabel.CODE, parent=parent_element, text=snippet_text
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)
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elif isinstance(element, marko.block.FencedCode):
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self.close_table(doc)
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self.process_inline_text(parent_element, doc)
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_log.debug(f" - Code Block: {element.children}")
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snippet_text = str(element.children[0].children).strip()
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doc.add_text(
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label=DocItemLabel.CODE, parent=parent_element, text=snippet_text
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)
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elif isinstance(element, marko.inline.LineBreak):
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self.process_inline_text(parent_element, doc)
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if self.in_table:
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_log.debug("Line break in a table")
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self.md_table_buffer.append("")
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elif isinstance(element, marko.block.HTMLBlock):
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self.process_inline_text(parent_element, doc)
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self.close_table(doc)
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_log.debug("HTML Block: {}".format(element))
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if (
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len(element.children) > 0
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): # If Marko doesn't return any content for HTML block, skip it
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snippet_text = str(element.children).strip()
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doc.add_text(
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label=DocItemLabel.CODE, parent=parent_element, text=snippet_text
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)
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else:
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if not isinstance(element, str):
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self.close_table(doc)
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_log.debug("Some other element: {}".format(element))
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# Iterate through the element's children (if any)
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if not isinstance(element, marko.block.ListItem):
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if not isinstance(element, marko.block.Heading):
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if not isinstance(element, marko.block.FencedCode):
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# if not isinstance(element, marko.block.Paragraph):
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if hasattr(element, "children"):
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for child in element.children:
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self.iterate_elements(child, depth + 1, doc, parent_element)
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def is_valid(self) -> bool:
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return self.valid
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def unload(self):
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if isinstance(self.path_or_stream, BytesIO):
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self.path_or_stream.close()
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self.path_or_stream = None
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@classmethod
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def supports_pagination(cls) -> bool:
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return False
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@classmethod
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def supported_formats(cls) -> Set[InputFormat]:
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return {InputFormat.MD}
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def convert(self) -> DoclingDocument:
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_log.debug("converting Markdown...")
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origin = DocumentOrigin(
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filename=self.file.name or "file",
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mimetype="text/markdown",
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binary_hash=self.document_hash,
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)
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doc = DoclingDocument(name=self.file.stem or "file", origin=origin)
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if self.is_valid():
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# Parse the markdown into an abstract syntax tree (AST)
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marko_parser = Markdown()
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parsed_ast = marko_parser.parse(self.markdown)
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# Start iterating from the root of the AST
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self.iterate_elements(parsed_ast, 0, doc, None)
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self.process_inline_text(None, doc) # handle last hanging inline text
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else:
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raise RuntimeError(
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f"Cannot convert md with {self.document_hash} because the backend failed to init."
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)
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return doc
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