diff --git a/pyproject.toml b/pyproject.toml index 86b76b4..2a70735 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,6 +12,7 @@ dependencies = [ "webalgebra", "pydantic>=2.0.0", "pydantic-settings>=2.0.0", + "lxml>=5.0.0", ] [build-system] diff --git a/src/scripts/push_arxiv_to_linkeddatahub.py b/src/scripts/push_arxiv_to_linkeddatahub.py index cc93f91..79f92c8 100644 --- a/src/scripts/push_arxiv_to_linkeddatahub.py +++ b/src/scripts/push_arxiv_to_linkeddatahub.py @@ -5,17 +5,148 @@ warnings.filterwarnings("ignore", category=UserWarning, module="pydantic._internal._generate_schema") import argparse -from urllib.parse import quote +import urllib.request +import urllib.error +from datetime import datetime from pydantic_settings import BaseSettings, SettingsConfigDict from pydantic import Field -from rdflib import Literal, Namespace, Dataset, URIRef, BNode -from rdflib.namespace import RDF, FOAF +import rdflib +from rdflib import Literal, Namespace, Dataset, URIRef, BNode, Graph +from rdflib.namespace import RDF, FOAF, XSD from tqdm import tqdm +from lxml import etree from ldh_bots.operations.feeds.arxiv import ArxivFeed from web_algebra.operations.linkeddatahub.create_item import CreateItem +from web_algebra.operations.linkeddatahub.content.add_xhtml_block import AddXHTMLBlock from web_algebra.operations.linked_data.post import POST SCHEMA = Namespace("http://schema.org/") +XHTML_NS = "http://www.w3.org/1999/xhtml" +MATHML_NS = "http://www.w3.org/1998/Math/MathML" + + +def parse_date_to_arxiv_format(date_str: str) -> str: + """Parse various date formats and convert to arXiv format (YYYYMMDDHHMM). + + Supported input formats: + - YYYY-MM-DD (time defaults to 00:00) + - YYYYMMDD (time defaults to 00:00) + - YYYY-MM-DD HH:MM + - YYYYMMDDHHMM (native arXiv format, returned as-is) + + Args: + date_str: Date string in one of the supported formats + + Returns: + Date in arXiv format (YYYYMMDDHHMM) + + Raises: + ValueError: If date format is not recognized + """ + date_str = date_str.strip() + + # Try native arXiv format first (YYYYMMDDHHMM) + if len(date_str) == 12 and date_str.isdigit(): + return date_str + + # Try YYYYMMDD format + if len(date_str) == 8 and date_str.isdigit(): + return date_str + "0000" + + # Try YYYY-MM-DD format + try: + dt = datetime.strptime(date_str, "%Y-%m-%d") + return dt.strftime("%Y%m%d0000") + except ValueError: + pass + + # Try YYYY-MM-DD HH:MM format + try: + dt = datetime.strptime(date_str, "%Y-%m-%d %H:%M") + return dt.strftime("%Y%m%d%H%M") + except ValueError: + pass + + raise ValueError( + f"Invalid date format: '{date_str}'. " + f"Supported formats: YYYY-MM-DD, YYYYMMDD, YYYY-MM-DD HH:MM, or YYYYMMDDHHMM" + ) + + +def fetch_arxiv_html(arxiv_id: str) -> str: + """Fetch HTML version of ArXiv paper. + + Args: + arxiv_id: ArXiv ID (e.g., "2510.12134v1") + + Returns: + HTML content as string, or None if not available + """ + url = f"https://arxiv.org/html/{arxiv_id}" + try: + req = urllib.request.Request(url) + with urllib.request.urlopen(req) as response: + return response.read().decode('utf-8') + except urllib.error.HTTPError as e: + if e.code == 404: + return None + raise + + +def extract_sections(html_content: str) -> list[tuple[str, etree._Element, str]]: + """Extract sections from ArXiv HTML. + + Args: + html_content: Full HTML document as string + + Returns: + List of tuples (section_id, section_element, section_title) + """ + root = etree.fromstring(html_content.encode('utf-8')) + sections = [] + + # Find all section elements + for section in root.xpath('//section[@id]'): + section_id = section.get('id') + + # Get section title from first heading + title_elem = section.find('.//*[@class="ltx_title"]') + section_title = "" + if title_elem is not None: + # Extract text content, removing tags + section_title = ''.join(title_elem.itertext()).strip() + + sections.append((section_id, section, section_title)) + + return sections + + +def wrap_and_serialize_c14n(section: etree._Element) -> str: + """Wrap section in XHTML div and serialize as canonical XML. + + Args: + section: Section element to wrap + + Returns: + C14N 2.0 serialized XHTML string (required for RDF XMLLiterals) + """ + from copy import deepcopy + import unicodedata + + # Create wrapper div with XHTML as default namespace (not prefixed) + wrapper = etree.Element(f"{{{XHTML_NS}}}div", nsmap={None: XHTML_NS}) + + # Deep copy the section + section_copy = deepcopy(section) + wrapper.append(section_copy) + + # Use C14N 2.0 (required for RDF XMLLiterals) + c14n_xml = etree.canonicalize(wrapper, with_comments=False) + + # Normalize Unicode to NFC form (canonical composition) + c14n_xml = unicodedata.normalize('NFC', c14n_xml) + + return c14n_xml class Settings(BaseSettings): @@ -41,8 +172,8 @@ class Settings(BaseSettings): parser.add_argument( "--container", type=str, - default="https://papers.localhost:4443/papers/", - help="LinkedDataHub container URL (default: https://papers.localhost:4443/papers/)" + default="https://papers.localhost:4443/arxiv/", + help="LinkedDataHub container URL (default: https://papers.localhost:4443/arxiv/)" ) parser.add_argument( "--cert", @@ -76,6 +207,18 @@ class Settings(BaseSettings): choices=["ascending", "descending"], help="Sort order (default: descending)" ) + parser.add_argument( + "--from-date", + type=str, + default=None, + help="Filter papers from this date (formats: YYYY-MM-DD, YYYYMMDD, YYYY-MM-DD HH:MM, or YYYYMMDDHHMM)" + ) + parser.add_argument( + "--to-date", + type=str, + default=None, + help="Filter papers up to this date (formats: YYYY-MM-DD, YYYYMMDD, YYYY-MM-DD HH:MM, or YYYYMMDDHHMM)" + ) args = parser.parse_args() @@ -88,11 +231,27 @@ class Settings(BaseSettings): # LinkedDataHub container URL container_url = URIRef(args.container) + # Construct date filter if provided + search_query = args.search_query + if args.from_date or args.to_date: + try: + from_date_str = parse_date_to_arxiv_format(args.from_date) if args.from_date else "190001010000" + to_date_str = parse_date_to_arxiv_format(args.to_date) if args.to_date else "209912312359" + + date_filter = f"submittedDate:[{from_date_str} TO {to_date_str}]" + # Combine with existing search query using AND + search_query = f"({args.search_query}) AND {date_filter}" + + print(f"Date filter applied: {date_filter}") + except ValueError as e: + print(f"Error parsing date: {e}") + exit(1) + # Step 1: Fetch ArXiv papers - print(f"Searching ArXiv for: '{args.search_query}'...") + print(f"Searching ArXiv for: '{search_query}'...") arxiv_feed = ArxivFeed(settings=settings, context={}) papers_dataset = arxiv_feed.execute( - search_query=Literal(args.search_query), + search_query=Literal(search_query), max_results=Literal(args.max_results), sort_by=Literal(args.sort_by), sort_order=Literal(args.sort_order) @@ -107,6 +266,7 @@ class Settings(BaseSettings): # Initialize operations create_item = CreateItem(settings=settings, context={}) post = POST(settings=settings, context={}) + add_xhtml_block = AddXHTMLBlock(settings=settings, context={}) paper_count = 0 @@ -119,6 +279,12 @@ class Settings(BaseSettings): print(f"Skipping graph without article") continue + # Get ArXiv ID for slug + arxiv_id = paper_graph.value(paper_blank_node, URIRef("http://arxiv.org/property/id")) + if not arxiv_id: + print(f"Skipping paper without ArXiv ID") + continue + title = paper_graph.value(paper_blank_node, SCHEMA.headline) if not title: title = paper_graph.value(paper_blank_node, SCHEMA.name) @@ -128,14 +294,14 @@ class Settings(BaseSettings): paper_count += 1 print(f"\n[{paper_count}] Processing: {title}") + print(f" ArXiv ID: {arxiv_id}") - # Step 2a: Create item in LinkedDataHub to get the item URL - slug = quote(str(title).lower().replace(" ", "-"), safe="") + # Step 2a: Create item in LinkedDataHub using ArXiv ID as slug try: result = create_item.execute( container_uri=container_url, title=Literal(str(title)), - slug=Literal(slug) + slug=Literal(str(arxiv_id)) ) item_url = result.bindings[0]["url"] print(f" Created item at: {item_url}") @@ -170,6 +336,54 @@ class Settings(BaseSettings): status = post_result.bindings[0]["status"] print(f" POST status: {status}") + # Step 2e: Fetch and add HTML sections if available + print(f" Fetching HTML version for {arxiv_id}...") + html_content = fetch_arxiv_html(str(arxiv_id)) + + if html_content: + print(f" Extracting sections from HTML...") + sections = extract_sections(html_content) + print(f" Found {len(sections)} sections") + + # Add each section as XHTML block + for section_id, section_elem, section_title in sections: + try: + print(f" Adding section {section_id}: {section_title[:50]}...") + + # Wrap and serialize as C14N + xhtml_content = wrap_and_serialize_c14n(section_elem) + + # Add XHTML block to LinkedDataHub + try: + # Workaround for RDFLib bug: Disable literal normalization to prevent + # minidom.toxml() from converting empty elements like
to + # which violates C14N and breaks Apache Jena 4.7.0 XMLLiteral validation + # See: https://github.com/RDFLib/rdflib/blob/main/rdflib/term.py#L1930 + rdflib.NORMALIZE_LITERALS = False + xml_literal = Literal(xhtml_content, datatype=RDF.XMLLiteral) + + add_xhtml_block.execute( + url=URIRef(item_url), + value=xml_literal, + title=Literal(section_title, datatype=XSD.string) if section_title else None, + fragment=Literal(section_id, datatype=XSD.string) + ) + + rdflib.NORMALIZE_LITERALS = True + except urllib.error.HTTPError as e: + error_body = e.read().decode('utf-8') if hasattr(e, 'read') else str(e) + print(f" Error adding section {section_id}: HTTP {e.code}") + print(f" Error body: {error_body[:200]}...") + continue + except Exception as e: + print(f" Error adding section {section_id}: {e}") + continue + except Exception as e: + print(f" Error processing section {section_id}: {e}") + continue + else: + print(f" HTML version not available for {arxiv_id}") + except Exception as e: 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