diff --git a/datasets/README.md b/datasets/README.md index 4b780977..37592504 100644 --- a/datasets/README.md +++ b/datasets/README.md @@ -5,3 +5,21 @@ Dataset ingestion, processing, and construction for the [Agentic Medical Fact Ve Covers ingesting and normalizing source corpora, generating synthetic data with frontier / top open models, building train / validation / test splits, and producing fact-database entries. Workspace member (`amfv-datasets`). + +## Optional dependencies + +Sources that publish guidelines as PDFs need the `pdf` extra, which installs +Docling for PDF-to-markdown conversion: + +```bash +uv sync --group pdf +``` + +Without it those scrapers still run but fall back to whatever HTML the landing +page exposes. See +[scraping/LICENSE_NOTES.md](amfv_datasets/scraping/LICENSE_NOTES.md) for how +`metadata.content_scope` reports this. + +Sample WHO guideline PDFs and the markdown extracted from them are committed in +`test/fixtures/pdf/`. See [benchmarks/README.md](benchmarks/README.md) for how +to inspect and verify the conversion, and why Docling is the default backend. diff --git a/datasets/amfv_datasets/scraping/LICENSE_NOTES.md b/datasets/amfv_datasets/scraping/LICENSE_NOTES.md new file mode 100644 index 00000000..8adb39b7 --- /dev/null +++ b/datasets/amfv_datasets/scraping/LICENSE_NOTES.md @@ -0,0 +1,62 @@ +# Source licensing notes for scraped corpora + +## WHO (World Health Organization) + +Publications on [who.int](https://www.who.int/publications) published since +November 2016 are licensed under **Creative Commons Attribution-NonCommercial- +ShareAlike 3.0 IGO** (CC BY-NC-SA 3.0 IGO). + +- **Non-commercial use and adaptation** are permitted. +- **Attribution** to WHO is required. +- **Share-alike**: derivatives must use the same or a similar licence. + +Pre-2017 publications were not reissued under this licence. Use +`metadata.publication_date` to filter when building corpora. + +### Suggested attribution + +> © World Health Organization {year}. *{publication title}*. +> Licensed under CC BY-NC-SA 3.0 IGO. +> https://creativecommons.org/licenses/by-nc-sa/3.0/igo/ + +Each scraped document also records `metadata.license` and +`metadata.attribution`. + +### Content scope + +The WHO scraper emits the HTML **Overview** from the publication landing page +followed by the guideline body converted from the linked PDF +(`metadata.download_url`). `metadata.content_scope` records which was captured: + +- `full` — Overview plus converted PDF body. `metadata.pdf_backend` and + `metadata.pdf_bytes` describe the conversion. +- `overview` — Overview only, because no PDF was linked, the download failed, or + conversion failed. Both PDF metadata fields are `null`. + +PDF conversion needs the optional `pdf` extra (`uv sync --group pdf`). Without +it every document degrades to `overview`, so check `content_scope` before +treating a corpus as full text. + +### Committed test fixtures + +`datasets/test/fixtures/pdf/` holds six-page excerpts of two WHO guidelines, so +conversion can be tested against real guideline text offline: + +| Fixture | Source | Pages | +| --- | --- | --- | +| `who_9789240121805_excerpt.pdf` | [Guidelines for the prevention of bloodstream infections and other infections associated with the use of intravascular catheters: part 2: central venous catheters](https://www.who.int/publications/i/item/9789240121805) | 30-35 | +| `who_9789240124233_excerpt.pdf` | [Consolidated HIV guidelines: service delivery](https://www.who.int/publications/i/item/9789240124233) | 11-16 | + +Each PDF sits next to a `.expected.md` file holding the markdown the scraper +extracts from it, so the conversion can be inspected without running anything. +Those markdown files are derivative works of the PDFs and carry the same licence. + +Both are redistributed unmodified apart from page selection, under CC BY-NC-SA +3.0 IGO: + +> © World Health Organization. Licensed under CC BY-NC-SA 3.0 IGO. +> https://creativecommons.org/licenses/by-nc-sa/3.0/igo/ + +They are test data for non-commercial research use. Note that this licence is +more restrictive than the repository's Apache-2.0 licence, which covers the code +only and does not extend to these files. diff --git a/datasets/amfv_datasets/scraping/__init__.py b/datasets/amfv_datasets/scraping/__init__.py index cd7cdb06..8d5fe252 100644 --- a/datasets/amfv_datasets/scraping/__init__.py +++ b/datasets/amfv_datasets/scraping/__init__.py @@ -27,6 +27,22 @@ scrape_guideline, scrape_nice, ) +from amfv_datasets.scraping.pdf import ( + PdfBackend, + PdfConversionError, + count_markdown_sections, + pdf_to_markdown, +) +from amfv_datasets.scraping.who import ( + WhoFetchError, + WhoListingPage, + WhoPublicationRef, + build_publication_text, + list_publications, + publication_ref_from_url, + scrape_publication, + scrape_who, +) __all__ = [ "GuidanceRef", @@ -34,21 +50,33 @@ "LinkMode", "NiceFetchError", "OutputFormat", + "PdfBackend", + "PdfConversionError", "ScrapeError", "ScrapeRun", "ScrapedDocument", "ScraperSource", "USER_AGENT", + "WhoFetchError", + "WhoListingPage", + "WhoPublicationRef", "absolute_unique_urls", "build_guideline_text", + "build_publication_text", "clean_text", + "count_markdown_sections", "document_title", "default_client", "first_matching_urls", "guidance_ref_from_url", "html_to_markdown", "list_published_guidance", + "list_publications", + "pdf_to_markdown", + "publication_ref_from_url", "scrape_guideline", "scrape_listing_documents", "scrape_nice", + "scrape_publication", + "scrape_who", ] diff --git a/datasets/amfv_datasets/scraping/cli.py b/datasets/amfv_datasets/scraping/cli.py index e8aece34..59e69bd7 100644 --- a/datasets/amfv_datasets/scraping/cli.py +++ b/datasets/amfv_datasets/scraping/cli.py @@ -27,6 +27,7 @@ from amfv_datasets.scraping.base import ScrapedDocument, ScrapeRun from amfv_datasets.scraping.html import LinkMode from amfv_datasets.scraping.nice import scrape_nice +from amfv_datasets.scraping.who import scrape_who class ScraperSource(StrEnum): @@ -34,6 +35,7 @@ class ScraperSource(StrEnum): ALL = "all" NICE = "nice" + WHO = "who" class OutputFormat(StrEnum): @@ -72,6 +74,8 @@ def scrape_documents( match selected_source: case ScraperSource.NICE: return scrape_nice(documents=documents, link_mode=link_mode, url=url) + case ScraperSource.WHO: + return scrape_who(documents=documents, link_mode=link_mode, url=url) case ScraperSource.ALL: raise AssertionError("expanded source cannot be all") raise AssertionError(f"unsupported source: {source}") @@ -125,7 +129,7 @@ def write_markdown_files(documents: Iterable[ScrapedDocument], output_path: Path def _expand_source(source: ScraperSource) -> tuple[ScraperSource, ...]: if source is ScraperSource.ALL: - return (ScraperSource.NICE,) + return (ScraperSource.NICE, ScraperSource.WHO) return (source,) diff --git a/datasets/amfv_datasets/scraping/pdf.py b/datasets/amfv_datasets/scraping/pdf.py new file mode 100644 index 00000000..10025de4 --- /dev/null +++ b/datasets/amfv_datasets/scraping/pdf.py @@ -0,0 +1,169 @@ +"""Convert source PDFs into markdown for scrapers. + +Some guideline publishers release the document body only as a PDF, so the HTML +page carries an abstract at best. These helpers convert such PDFs into the same +clean markdown the HTML scrapers produce. + +Docling is the default backend. On a five-document sample of WHO guidelines it +preserved GRADE evidence-table rows that Marker dropped, emitted no stray page +numbers where PyMuPDF4LLM emitted roughly twenty per excerpt, and recovered the +most heading structure. It also runs on CPU, which keeps the scrapers usable +without a GPU. See `datasets/benchmarks/README.md` for the measurements and +`datasets/benchmarks/pdf_backends.py` to reproduce them. +""" + +from __future__ import annotations + +import logging +import re +from enum import StrEnum +from io import BytesIO + +from amfv_datasets.scraping.base import ScrapeError + +try: + from docling.datamodel.base_models import DocumentStream, InputFormat + from docling.datamodel.pipeline_options import PdfPipelineOptions + from docling.document_converter import DocumentConverter, PdfFormatOption + + HAS_DOCLING = True +except ImportError: + HAS_DOCLING = False + +logger = logging.getLogger(__name__) + +MIN_RUNNING_HEADER_CHARS = 20 +"""Shortest title fragment treated as a running header rather than content.""" + +_HEADING_RE = re.compile(r"^(#{1,6})\s+\S") +_BLANK_LINES_RE = re.compile(r"\n{3,}") + + +class PdfBackend(StrEnum): + """Supported PDF-to-markdown conversion backends.""" + + DOCLING = "docling" + + +class PdfConversionError(ScrapeError): + """Raised when a PDF cannot be converted to markdown.""" + + +_DOCLING_CONVERTERS: dict[bool, DocumentConverter] = {} + + +def _docling_converter(*, ocr: bool) -> DocumentConverter: + """Return a cached Docling converter, since model load is expensive.""" + converter = _DOCLING_CONVERTERS.get(ocr) + if converter is None: + options = PdfPipelineOptions() + options.do_ocr = ocr + options.do_table_structure = True + options.table_structure_options.do_cell_matching = True + converter = DocumentConverter(format_options={InputFormat.PDF: PdfFormatOption(pipeline_options=options)}) + _DOCLING_CONVERTERS[ocr] = converter + return converter + + +def pdf_to_markdown( + data: bytes, + *, + backend: PdfBackend = PdfBackend.DOCLING, + ocr: bool = False, + running_header: str | None = None, + name: str = "document.pdf", +) -> str: + """Convert PDF bytes into markdown. + + Args: + data: Raw PDF bytes. + backend: Conversion backend to use (default: PdfBackend.DOCLING). + ocr: Whether to run OCR. Leave disabled for born-digital PDFs, where it + only adds runtime (default: False). + running_header: Repeated page header to drop from the output, usually the + document title (default: None). + name: File name reported to the backend, used for logging and format + detection (default: "document.pdf"). + """ + if not data: + raise PdfConversionError("Cannot convert an empty PDF payload") + if backend is not PdfBackend.DOCLING: + raise PdfConversionError(f"Unsupported PDF backend: {backend}") + if not HAS_DOCLING: + raise PdfConversionError("Docling is required to convert PDFs; install it with `uv sync --extra pdf`") + + try: + result = _docling_converter(ocr=ocr).convert(DocumentStream(name=name, stream=BytesIO(data))) + markdown = result.document.export_to_markdown() + except Exception as exc: # noqa: BLE001 - backend raises library-specific errors + raise PdfConversionError(f"Could not convert PDF '{name}': {exc}") from exc + + markdown = _strip_running_header(markdown, running_header) + if not markdown.strip(): + raise PdfConversionError(f"PDF '{name}' produced no readable markdown") + return markdown + + +def count_markdown_sections(markdown: str) -> int: + """Count sections in markdown by its shallowest heading level. + + Args: + markdown: Markdown text to inspect. + """ + levels = [len(match.group(1)) for line in markdown.splitlines() if (match := _HEADING_RE.match(line.strip()))] + if not levels: + return 1 + top_level = min(levels) + return sum(1 for level in levels if level == top_level) + + +def _collapse_repeated_text(text: str) -> str: + """Reduce text built from a repeated phrase to a single copy. + + Left and right page headers often land on one line, so a running header + arrives doubled. + """ + words = text.split() + for parts in (2, 3, 4): + if len(words) < parts or len(words) % parts: + continue + size = len(words) // parts + chunk = words[:size] + if all(words[index * size : (index + 1) * size] == chunk for index in range(parts)): + return " ".join(chunk) + return text + + +def _strip_running_header(markdown: str, running_header: str | None) -> str: + """Drop standalone lines repeating a PDF running header. + + A line is dropped only when it is a long prefix of the title or the title is + a prefix of it, because publishers shorten the title in page headers. Lines + such as "(Strong recommendation, moderate-certainty evidence)" repeat + legitimately and must survive. + """ + if not running_header: + return markdown.strip() + + needle = " ".join(running_header.split()).casefold() + if not needle: + return markdown.strip() + + kept: list[str] = [] + for line in markdown.splitlines(): + candidate = _collapse_repeated_text(" ".join(line.split()).casefold().strip("# ")) + is_header = len(candidate) >= MIN_RUNNING_HEADER_CHARS and ( + needle.startswith(candidate) or candidate.startswith(needle) + ) + if not is_header: + kept.append(line) + return _BLANK_LINES_RE.sub("\n\n", "\n".join(kept)).strip() + + +__all__ = [ + "HAS_DOCLING", + "PdfBackend", + "PdfConversionError", + "count_markdown_sections", + "pdf_to_markdown", +] diff --git a/datasets/amfv_datasets/scraping/who.py b/datasets/amfv_datasets/scraping/who.py new file mode 100644 index 00000000..5c7a8ad2 --- /dev/null +++ b/datasets/amfv_datasets/scraping/who.py @@ -0,0 +1,474 @@ +"""Scrape WHO guideline publications into normalized markdown documents. + +WHO (World Health Organization) publishes guidelines primarily as PDFs hosted on +iris.who.int. The publication landing page carries only a short HTML Overview, +so the guideline body itself comes from the linked PDF, converted to markdown by +`amfv_datasets.scraping.pdf`. Each document is the Overview followed by the +converted guideline text; `metadata["content_scope"]` records whether the full +body was recovered. + +Sampled WHO guideline PDFs are born-digital with a clean text layer, so +conversion runs without OCR. + +Discovery uses WHO's Sitefinity OData publications hub API, filtered to the +Guidelines publishing office. + +Attribution: +The publishing-office filter UUID and PDF-first approach in Meditron's WHO +scraper (epfLLM/meditron, gap-replay/guidelines/scrapers/scrapers.py) informed +discovery scope. Source license: Apache License 2.0. +""" + +from __future__ import annotations + +import json +import logging +import re +from collections.abc import Callable, Iterable +from dataclasses import dataclass +from typing import Any +from urllib.parse import urlparse + +import httpx +from lxml import html as lxml_html + +from amfv_datasets.scraping.base import ( + ScrapedDocument, + ScrapeError, + ScrapeRun, + default_client, + scrape_listing_documents, +) +from amfv_datasets.scraping.html import LinkMode, clean_text, document_title, html_to_markdown +from amfv_datasets.scraping.pdf import ( + PdfBackend, + PdfConversionError, + count_markdown_sections, + pdf_to_markdown, +) + +BASE_URL = "https://www.who.int" +GUIDELINES_LISTING_URL = f"{BASE_URL}/publications/who-guidelines" +GUIDELINES_PUBLISHING_OFFICE = "c09761c0-ab8e-4cfa-9744-99509c4d306b" +SF_SITE = "15210d59-ad60-47ff-a542-7ed76645f0c7" +PUBLICATIONS_API_PATH = "/api/hubs/publications" +LISTING_PAGE_SIZE = 25 +DOCUMENT_DELAY_SECONDS = 5.0 +WHO_LICENSE = "CC BY-NC-SA 3.0 IGO" +WHO_ATTRIBUTION = "© World Health Organization. Licensed under CC BY-NC-SA 3.0 IGO." +CONTENT_SCOPE_FULL = "full" +CONTENT_SCOPE_OVERVIEW = "overview" +PDF_TIMEOUT_SECONDS = 180.0 + +type PdfMarkdownConverter = Callable[[bytes, str, str], str] + +logger = logging.getLogger(__name__) + +_PUBLICATION_PATH_RE = re.compile( + r"^/publications/i/item/(?P[^/?#]+)(?:/|$)", + re.IGNORECASE, +) +_ISBN_RE = re.compile(r"ISBN:\s*([\d\-]+)", re.IGNORECASE) + + +class WhoFetchError(ScrapeError): + """Raised when a WHO publication cannot be fetched or parsed.""" + + +@dataclass(frozen=True) +class WhoPublicationRef: + """A WHO guideline publication reference from the listing.""" + + publication_id: str + title: str + page_url: str + publication_date: str | None = None + tag: str | None = None + download_url: str | None = None + + +@dataclass(frozen=True) +class WhoListingPage: + """A page of WHO guideline publication references.""" + + refs: list[WhoPublicationRef] + total: int | None + + +def publication_ref_from_url(url: str) -> WhoPublicationRef: + """Parse a WHO publication URL into a canonical publication reference. + + Args: + url: WHO publication URL to parse. + """ + parsed = urlparse(url.strip()) + if parsed.scheme not in {"http", "https"} or parsed.netloc.lower() not in { + "www.who.int", + "who.int", + }: + raise WhoFetchError(f"Enter a WHO publication URL from who.int; got {url!r}") + + match = _PUBLICATION_PATH_RE.match(parsed.path.rstrip("/") + "/") + if not match: + raise WhoFetchError(f"Enter a URL like https://www.who.int/publications/i/item/9789240121805; got {url!r}") + + publication_id = match.group("publication_id") + return WhoPublicationRef( + publication_id=publication_id, + title=publication_id, + page_url=_page_url(publication_id=publication_id), + ) + + +def _page_url(*, publication_id: str) -> str: + return f"{BASE_URL}/publications/i/item/{publication_id}" + + +def _publications_api_params(*, page: int) -> dict[str, str]: + skip = (page - 1) * LISTING_PAGE_SIZE + return { + "sf_site": SF_SITE, + "sf_provider": "OpenAccessProvider", + "sf_culture": "en", + "$orderby": "PublicationDateAndTime desc", + "$select": "Title,ItemDefaultUrl,FormatedDate,Tag,DownloadUrl", + "$filter": f"publishingoffices/any(s:s eq {GUIDELINES_PUBLISHING_OFFICE})", + "$top": str(LISTING_PAGE_SIZE), + "$skip": str(skip), + "$count": "true", + } + + +def _publication_id_from_item_url(item_default_url: str) -> str: + return item_default_url.strip("/").split("/")[-1] + + +def _parse_api_listing(payload: dict[str, Any]) -> WhoListingPage: + """Parse a WHO publications OData response into listing refs.""" + try: + items = payload["value"] + except KeyError as exc: + raise WhoFetchError("Could not parse WHO publications API JSON") from exc + + refs: list[WhoPublicationRef] = [] + for item in items: + item_default_url = (item.get("ItemDefaultUrl") or "").strip() + title = (item.get("Title") or "").strip() + if not item_default_url or not title: + continue + publication_id = _publication_id_from_item_url(item_default_url) + refs.append( + WhoPublicationRef( + publication_id=publication_id, + title=title, + page_url=_page_url(publication_id=publication_id), + publication_date=(item.get("FormatedDate") or None), + tag=(item.get("Tag") or None), + download_url=(item.get("DownloadUrl") or None), + ) + ) + + total = payload.get("@odata.count") + return WhoListingPage(refs=refs, total=total if isinstance(total, int) else None) + + +def _parse_html_listing(html_text: str) -> WhoListingPage: + """Parse server-rendered WHO guideline cards from the listing page.""" + doc = lxml_html.fromstring(html_text) + refs: list[WhoPublicationRef] = [] + seen: set[str] = set() + for link in doc.xpath("//a[contains(@href,'/publications/i/item/')]"): + href = link.get("href", "").split("?")[0] + match = _PUBLICATION_PATH_RE.match(href.rstrip("/") + "/") + if not match or href in seen: + continue + seen.add(href) + publication_id = match.group("publication_id") + title = clean_text(link.xpath("string(.)")) or publication_id + refs.append( + WhoPublicationRef( + publication_id=publication_id, + title=title, + page_url=_page_url(publication_id=publication_id), + ) + ) + return WhoListingPage(refs=refs, total=None) + + +def list_publications(client: httpx.Client, page: int = 1) -> WhoListingPage: + """Return one page of WHO guideline publication refs. + + Args: + client: HTTP client used to fetch the publications API. + page: Listing page number (default: 1). + """ + response = client.get(f"{BASE_URL}{PUBLICATIONS_API_PATH}", params=_publications_api_params(page=page)) + if response.status_code >= 400: + logger.warning("WHO publications API returned %s; falling back to HTML listing", response.status_code) + listing = client.get(GUIDELINES_LISTING_URL) + listing.raise_for_status() + return _parse_html_listing(listing.text) + + try: + payload = response.json() + except json.JSONDecodeError as exc: + raise WhoFetchError("Could not decode WHO publications API JSON") from exc + return _parse_api_listing(payload) + + +def _overview_html(section: lxml_html.HtmlElement) -> str: + """Return HTML for the Overview block within a publication section.""" + overview_headings = section.xpath(".//h3[normalize-space()='Overview']") + if not overview_headings: + return lxml_html.tostring(section, encoding="unicode") + + heading = overview_headings[0] + parts = [lxml_html.tostring(heading, encoding="unicode")] + sibling = heading.getnext() + while sibling is not None and sibling.tag.lower() not in {"h2", "h3"}: + parts.append(lxml_html.tostring(sibling, encoding="unicode")) + sibling = sibling.getnext() + return "".join(parts) + + +def _page_isbn(html_text: str) -> str | None: + doc = lxml_html.fromstring(html_text) + for node in doc.xpath("//*[contains(normalize-space(.), 'ISBN')]"): + match = _ISBN_RE.search(node.text_content()) + if match: + return match.group(1) + return None + + +def _page_publication_date(doc: lxml_html.HtmlElement) -> str | None: + values = doc.xpath("//*[contains(@class,'dynamic-content__date')]/text()") + return clean_text(values[0]) if values else None + + +def _page_tag(doc: lxml_html.HtmlElement) -> str | None: + values = doc.xpath("//*[contains(@class,'dynamic-content__tag')]/text()") + text = clean_text(" ".join(values)) + return text.lstrip("| ").strip() if text else None + + +def _page_download_url(doc: lxml_html.HtmlElement) -> str | None: + for href in doc.xpath("//a[contains(@href,'iris.who.int')]/@href"): + if "bitstreams" in href: + return href.split("?")[0] + return None + + +def _convert_guideline_pdf(data: bytes, title: str, publication_id: str) -> str: + """Convert a downloaded WHO guideline PDF into markdown.""" + return pdf_to_markdown(data, running_header=title, name=f"{publication_id}.pdf") + + +def _guideline_body( + client: httpx.Client, + ref: WhoPublicationRef, + *, + title: str, + download_url: str, + pdf_converter: PdfMarkdownConverter, +) -> tuple[str, int] | None: + """Download and convert a guideline PDF, or return None when unavailable. + + A single unconvertible PDF must not abort a long listing run, so transport + and conversion failures are logged and reported as a missing body. + """ + try: + response = client.get(download_url, timeout=PDF_TIMEOUT_SECONDS) + response.raise_for_status() + payload = response.content + body = pdf_converter(payload, title, ref.publication_id).strip() + except (httpx.HTTPError, PdfConversionError) as exc: + logger.warning("Falling back to Overview for '%s': %s", ref.publication_id, exc) + return None + if not body: + logger.warning("PDF for '%s' produced no markdown; falling back to Overview", ref.publication_id) + return None + return body, len(payload) + + +def build_publication_text( + client: httpx.Client, + ref: WhoPublicationRef, + *, + link_mode: LinkMode = LinkMode.KEEP, + include_full_text: bool = True, + pdf_converter: PdfMarkdownConverter | None = None, +) -> tuple[str, int, str, dict[str, Any]]: + """Scrape a publication into markdown text and bibliographic metadata. + + The Overview from the landing page leads, followed by the guideline body + converted from the linked PDF when one is available. + + Args: + client: HTTP client used to fetch the publication page and PDF. + ref: WHO publication reference to scrape. + link_mode: Whether links are kept as markdown links or stripped to their + visible text (default: LinkMode.KEEP). + include_full_text: Whether to download and convert the guideline PDF. + Disable for a fast Overview-only scrape (default: True). + pdf_converter: Converter receiving PDF bytes, title and publication id. + Defaults to the Docling-backed converter (default: None). + """ + response = client.get(ref.page_url) + response.raise_for_status() + html_text = response.text + doc = lxml_html.fromstring(html_text) + + sections = doc.xpath("//section[contains(@class,'dynamic-content__section')]") + if not sections: + raise WhoFetchError(f"No publication content section for '{ref.publication_id}'") + + title = ref.title if ref.title != ref.publication_id else document_title(html_text, fallback=ref.publication_id) + overview_html = _overview_html(sections[0]) + overview = html_to_markdown(overview_html, link_mode=link_mode, base_url=BASE_URL).strip() + if not overview: + raise WhoFetchError(f"No readable Overview content for '{ref.publication_id}'") + + download_url = ref.download_url or _page_download_url(doc) + body: tuple[str, int] | None = None + if include_full_text and download_url: + body = _guideline_body( + client, + ref, + title=title, + download_url=download_url, + pdf_converter=pdf_converter or _convert_guideline_pdf, + ) + elif include_full_text: + logger.warning("No PDF link for '%s'; emitting Overview only", ref.publication_id) + + content = f"{overview}\n\n{body[0]}" if body else overview + section_count = 1 + count_markdown_sections(body[0]) if body else 1 + + extra_metadata: dict[str, Any] = { + "publication_date": ref.publication_date or _page_publication_date(doc), + "tag": ref.tag or _page_tag(doc), + "isbn": _page_isbn(html_text), + "download_url": download_url, + "content_scope": CONTENT_SCOPE_FULL if body else CONTENT_SCOPE_OVERVIEW, + "pdf_backend": PdfBackend.DOCLING.value if body else None, + "pdf_bytes": body[1] if body else None, + "license": WHO_LICENSE, + "attribution": WHO_ATTRIBUTION, + "listing_category": "who-guidelines", + } + return content, section_count, title, extra_metadata + + +def scrape_publication( + client: httpx.Client, + ref: WhoPublicationRef, + *, + link_mode: LinkMode = LinkMode.KEEP, + include_full_text: bool = True, + pdf_converter: PdfMarkdownConverter | None = None, +) -> ScrapedDocument: + """Scrape a WHO publication into a normalized document. + + Args: + client: HTTP client used to fetch the publication page and PDF. + ref: WHO publication reference to scrape. + link_mode: Whether links are kept as markdown links or stripped to their + visible text (default: LinkMode.KEEP). + include_full_text: Whether to download and convert the guideline PDF + (default: True). + pdf_converter: Converter receiving PDF bytes, title and publication id. + Defaults to the Docling-backed converter (default: None). + """ + content, section_count, title, metadata = build_publication_text( + client, + ref, + link_mode=link_mode, + include_full_text=include_full_text, + pdf_converter=pdf_converter, + ) + return ScrapedDocument( + source="who", + external_id=f"who-{ref.publication_id}", + title=title, + url=ref.page_url, + content=content, + section_count=section_count, + metadata={ + "publication_id": ref.publication_id, + **metadata, + }, + ) + + +def scrape_who( + *, + documents: int | None, + link_mode: LinkMode = LinkMode.KEEP, + url: str | None = None, + include_full_text: bool = True, +) -> ScrapeRun: + """Scrape WHO documents from a URL or guideline listing pages. + + Args: + documents: Number of documents to scrape. Ignored when `url` is set. + When unset, WHO listing pages are fetched until a page returns no + items (default: None). + link_mode: Whether links are kept as markdown links or stripped to their + visible text (default: LinkMode.KEEP). + url: WHO publication URL to scrape as a single document (default: None). + include_full_text: Whether to download and convert each guideline PDF. + Requires the `pdf` extra; without it documents fall back to the + Overview (default: True). + """ + if url is not None: + + def scrape_url() -> Iterable[ScrapedDocument]: + with default_client() as client: + yield scrape_publication( + client, + publication_ref_from_url(url), + link_mode=link_mode, + include_full_text=include_full_text, + ) + + return ScrapeRun(documents=scrape_url(), total=1) + + with default_client() as client: + first_page = list_publications(client, page=1) + total = first_page.total if documents is None or first_page.total is None else min(documents, first_page.total) + return ScrapeRun( + total=total, + documents=scrape_listing_documents( + documents=documents, + client_factory=default_client, + first_page_items=first_page.refs, + list_page=lambda client, page: list_publications(client, page).refs, + scrape_item=lambda client, ref: scrape_publication( + client, + ref, + link_mode=link_mode, + include_full_text=include_full_text, + ), + document_delay_seconds=DOCUMENT_DELAY_SECONDS, + ), + ) + + +__all__ = [ + "BASE_URL", + "CONTENT_SCOPE_FULL", + "CONTENT_SCOPE_OVERVIEW", + "DOCUMENT_DELAY_SECONDS", + "GUIDELINES_LISTING_URL", + "PdfMarkdownConverter", + "WHO_ATTRIBUTION", + "WHO_LICENSE", + "WhoFetchError", + "WhoListingPage", + "WhoPublicationRef", + "build_publication_text", + "list_publications", + "publication_ref_from_url", + "scrape_publication", + "scrape_who", +] diff --git a/datasets/benchmarks/README.md b/datasets/benchmarks/README.md new file mode 100644 index 00000000..291fefc4 --- /dev/null +++ b/datasets/benchmarks/README.md @@ -0,0 +1,131 @@ +# PDF backend comparison + +Why `amfv_datasets.scraping.pdf` defaults to Docling. + +WHO publishes guidelines as PDFs and exposes only a short Overview on the +landing page, so the guideline body has to come from the PDF. Picking the +converter is a correctness decision rather than a formatting one: a backend that +silently drops rows from a GRADE evidence table produces text that reads fine +but states the wrong thing, which is the worst possible failure for fact +verification. + +## Sample + +Five WHO guidelines, chosen for a spread of length and table density. All five +are born-digital with a clean text layer (0-2 near-empty pages out of 25 +sampled per document), so OCR is pure overhead and is disabled. + +| Publication | Guideline | Pages | +| --- | --- | --- | +| 9789240121805 | Prevention of bloodstream infections, part 2: central venous catheters | 152 | +| 9789240124233 | Consolidated HIV guidelines: service delivery | 50 | +| 9789240073593 | Carbohydrate intake for adults and children | 100 | +| 9789240084278 | Mental health policy and strategic action plan | 184 | +| 9789241597906 | Hand hygiene in health care | 270 | + +Backends were run over a comparable page excerpt of each document. + +## Results + +Measured on an Apple Silicon laptop, CPU only. + +| Backend | Docs converted | Seconds per doc | Stray page-number lines | Notes | +| --- | --- | --- | --- | --- | +| Docling | 5 / 5 | 2.7-13.7 warm, 126.5 first run | 0 | Chosen | +| PyMuPDF4LLM | 5 / 5 | 1.9-5.1 | 40 across 2 docs | Fastest, corrupts table headers | +| Marker | spot check only | 72.7 | 0 | Drops table rows | +| MinerU | not run | - | - | Ruled out on cost after Docling met the bar | + +Docling's 126.5 s first run is one-off model loading; later documents in the +same process took 2.7-13.7 s. + +### Why not PyMuPDF4LLM + +It is the fastest option and its table row counts are close to Docling's, but it +emitted 40 bare page-number lines across two documents and corrupted table +header rows. Stray page numbers become sentence fragments once a document is +chunked for retrieval. + +### Why not Marker + +On the table-dense carbohydrate guideline Marker recovered 87 table rows where +Docling and PyMuPDF4LLM both found ~136, dropping outcome-category rows from a +GRADE evidence table. The loss is silent: the surrounding prose is intact, so +nothing signals that the evidence table is now incomplete. It was also the +slowest at 72.7 s per document. + +### Honest caveat + +On 9789240084278 PyMuPDF4LLM emitted 42 table rows against Docling's 13. That +gap was not spot-checked, so it is not established which is closer to the +source. It did not change the decision, since the Marker and PyMuPDF4LLM +failures above are disqualifying on their own, but it is the open question if +someone revisits this. + +## Decision + +Docling. It converted all five documents, recovered the most heading structure, +left no page furniture in the output, preserved table rows, and runs on CPU so +contributors and CI do not need a GPU. It is MIT licensed. + +## Seeing the extraction for yourself + +`datasets/test/fixtures/pdf/` holds each sample PDF next to the markdown the +scraper produces from it: + +| Input PDF | Extracted output | +| --- | --- | +| `who_9789240121805_excerpt.pdf` | `who_9789240121805_excerpt.expected.md` | +| `who_9789240124233_excerpt.pdf` | `who_9789240124233_excerpt.expected.md` | + +Open the two side by side to judge the conversion without running anything. The +first shows a GRADE recommendation keeping its certainty rating; the second +shows a recommendation table keeping its rows and columns. + +## Verifying + +Three layers, so CI never depends on a PDF stack: + +**1. Always runs, including CI.** `uv run pytest` covers the scraper wiring with +a stub converter. CI installs only `--group dev`, so the PDF tests report as +skipped and a Docling release cannot break the build. + +**2. Real conversion, opt-in.** Installs Docling and converts the sample PDFs +for real: + +```bash +uv sync --group pdf +uv run --group pdf pytest datasets/test/test_scraping_pdf_fixtures.py -v +``` + +These assert on meaning rather than formatting — that the recommendation text, +its certainty rating and its table rows are present — so they tolerate a Docling +upgrade that reflows whitespace. + +**3. Byte-exact diff, opt-in.** Compares conversion against the committed +`.expected.md` files: + +```bash +AMFV_CHECK_GOLDEN=1 uv run --group pdf pytest datasets/test/test_scraping_pdf_fixtures.py +``` + +This one is intentionally sensitive to the Docling version, which is why it is +off by default. If a Docling upgrade changes the output, review the diff and +then accept it: + +```bash +AMFV_UPDATE_GOLDEN=1 uv run --group pdf pytest datasets/test/test_scraping_pdf_fixtures.py +``` + +The regenerated `.expected.md` files then show the change in review. + +## Reproducing the benchmark + +```bash +uv sync --group pdf +uv run --group pdf python datasets/benchmarks/pdf_backends.py +``` + +That runs against the committed excerpt fixtures. Pass `--pdf-dir` to point at +full guideline PDFs, and `--backend` to select backends. Marker and MinerU are +not project dependencies; install them separately to include them. diff --git a/datasets/benchmarks/pdf_backends.py b/datasets/benchmarks/pdf_backends.py new file mode 100644 index 00000000..55b13b37 --- /dev/null +++ b/datasets/benchmarks/pdf_backends.py @@ -0,0 +1,139 @@ +"""Compare PDF-to-markdown backends on WHO guideline PDFs. + +Reproduces the measurements in `README.md` that led to Docling being the default +backend in `amfv_datasets.scraping.pdf`. Runs against the committed excerpt +fixtures by default, so it works offline: + + uv run --group pdf python datasets/benchmarks/pdf_backends.py + +Point it at full guideline PDFs for a heavier comparison: + + uv run --group pdf python datasets/benchmarks/pdf_backends.py --pdf-dir /tmp/who-pdfs + +Backends that are not installed are reported as skipped rather than failing the +run. Marker and MinerU are not project dependencies; install them separately to +include them. +""" + +from __future__ import annotations + +import argparse +import re +import time +from collections.abc import Callable +from pathlib import Path + +from amfv_datasets.scraping.pdf import pdf_to_markdown + +DEFAULT_PDF_DIR = Path(__file__).resolve().parents[1] / "test" / "fixtures" / "pdf" +_STRAY_PAGE_NUMBER_RE = re.compile(r"\s*\d{1,3}\s*") + + +def convert_docling(path: Path) -> str: + """Convert with the backend the scrapers actually ship. + + Args: + path: PDF to convert. + """ + return pdf_to_markdown(path.read_bytes(), name=path.name) + + +def convert_pymupdf4llm(path: Path) -> str: + """Convert with PyMuPDF4LLM. + + Args: + path: PDF to convert. + """ + import pymupdf4llm + + return pymupdf4llm.to_markdown(str(path)) + + +def convert_marker(path: Path) -> str: + """Convert with Marker. + + Args: + path: PDF to convert. + """ + from marker.converters.pdf import PdfConverter + from marker.models import create_model_dict + from marker.output import text_from_rendered + + converter = PdfConverter(artifact_dict=create_model_dict(), config={"pdftext_workers": 1}) + text, _, _ = text_from_rendered(converter(str(path))) + return text + + +BACKENDS: dict[str, Callable[[Path], str]] = { + "docling": convert_docling, + "pymupdf4llm": convert_pymupdf4llm, + "marker": convert_marker, +} + + +def measure(markdown: str) -> dict[str, int]: + """Score converted markdown on structure recovery and page furniture. + + Table rows matter most: a backend that silently drops rows from a GRADE + evidence table produces text that reads fine but states the wrong thing. + + Args: + markdown: Converted markdown to score. + """ + lines = markdown.splitlines() + return { + "chars": len(markdown), + "headings": sum(1 for line in lines if line.strip().startswith("#")), + "table_rows": sum(1 for line in lines if line.strip().startswith("|")), + "stray_page_numbers": sum(1 for line in lines if _STRAY_PAGE_NUMBER_RE.fullmatch(line)), + } + + +def run(pdf_dir: Path, backend_names: list[str]) -> None: + """Convert every PDF in a directory with each backend and print the scores. + + Args: + pdf_dir: Directory of PDFs to convert. + backend_names: Backends to run. + """ + pdfs = sorted(pdf_dir.glob("*.pdf")) + if not pdfs: + raise SystemExit(f"No PDFs found in {pdf_dir}") + + header = f"{'backend':<13}{'document':<34}{'secs':>7}{'chars':>9}{'head':>6}{'rows':>6}{'stray':>7}" + print(header) + print("-" * len(header)) + for name in backend_names: + for pdf in pdfs: + started = time.perf_counter() + try: + scores = measure(BACKENDS[name](pdf)) + except ImportError: + print(f"{name:<13}{'(not installed)':<34}") + break + except Exception as exc: # noqa: BLE001 - backends raise library-specific errors + print(f"{name:<13}{pdf.stem[:33]:<34} FAILED {str(exc)[:60]}") + continue + elapsed = time.perf_counter() - started + print( + f"{name:<13}{pdf.stem[:33]:<34}{elapsed:>7.1f}{scores['chars']:>9}" + f"{scores['headings']:>6}{scores['table_rows']:>6}{scores['stray_page_numbers']:>7}" + ) + + +def main() -> None: + """Parse arguments and run the comparison.""" + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--pdf-dir", type=Path, default=DEFAULT_PDF_DIR, help="directory of PDFs to convert") + parser.add_argument( + "--backend", + action="append", + choices=sorted(BACKENDS), + help="backend to run; repeatable, defaults to all", + ) + args = parser.parse_args() + run(args.pdf_dir, args.backend or sorted(BACKENDS)) + + +if __name__ == "__main__": + main() diff --git a/datasets/pyproject.toml b/datasets/pyproject.toml index 5638afb2..9dbcab42 100644 --- a/datasets/pyproject.toml +++ b/datasets/pyproject.toml @@ -13,6 +13,9 @@ dependencies = [ "typer>=0.12.0,<1.0.0", ] +[project.optional-dependencies] +pdf = ["docling>=2.119.0,<3.0.0"] + [project.scripts] amfv-scrape = "amfv_datasets.scraping.cli:main" diff --git a/datasets/test/fixtures/pdf/who_9789240121805_excerpt.expected.md b/datasets/test/fixtures/pdf/who_9789240121805_excerpt.expected.md new file mode 100644 index 00000000..c7f98cf1 --- /dev/null +++ b/datasets/test/fixtures/pdf/who_9789240121805_excerpt.expected.md @@ -0,0 +1,150 @@ +## 3.2 Pre-insertion + +## 3.2.1 Chlorhexidine-containing body wash + +- Recommendation 1. WHO suggests using a chlorhexidine-containing body wash (liquid or impregnated wipes) daily in critically-ill adults, adolescents and children. (Conditional recommendation, low certainly of evidence) + +## Remarks + +- The evidence did not differentiate between liquid and impregnated wipes and evaluated chlorhexidine concentrations ranging from 2% to 4%. It was noted that most of the studies provided evidence on the use of chlorhexidine, hence a decision was made to restrict the recommendation to chlorhexidine only and to adults, adolescents and children, but not neonates (due to the risk of chemical burns) (32) . +- The GDG noted that the use of this intervention would be particularly beneficial in settings with high baseline CLABSI rates. However, the GDG highlighted the need to prioritize resources at the local level based on other competing needs in the health care facility. The GDG also expressed concerns on the potential development of resistance to chlorhexidine and on waste generation when using wipes. +- Chlorhexidine products should be used with caution in patients with burns and according to the manufacturer's instructions in order to ensure they are safe for use . + +## Rationale for the recommendation + +Overall, the GDG judged both the desirable and undesirable effects to be small, but with a balance of effects probably favouring the intervention, with a low certainty of evidence. Based on the evidence provided, the GDG opted for a conditional recommendation in favour of the intervention, in particular in the context of high CLABSI rates at baseline, where the overall benefit may be more noticeable. + +## Summary of the evidence + +The Systematic Reviews Group identified 31 studies (10 randomized controlled trials [RCTs] (33-42) and 21 non-randomized studies of interventions [NRSIs] (43-63) ) comparing daily antiseptic body washing with chlorhexidine to soap and water bathing in adults, adolescents and children. + +- There was low certainty of evidence that daily antiseptic body washing may result in fewer CLABSI than no routine antiseptic body washing (risk ratio [RR]: 0.67; 95% confidence interval [CI]: 0.45 to 0.99; 10 RCTs (33-42) ). +- There was low certainty of evidence that routine antiseptic body washing may result in lower catheter-related mortality than no routine antiseptic body washing (RR: 0.20; 95% CI: 0.01 to 4.13; one RCT (41) ). +- There was low certainty of evidence that routine antiseptic body washing may result in little to no difference in all-cause mortality when compared with no routine antiseptic body washing (odds ratio [OR]: 0.90; 95% CI: 0.76 to 1.07; five RCTs (33, 37-40) ). +- There was very low certainty of evidence that routine antiseptic body washing may result in little to no difference in sepsis when compared with no routine antiseptic body washing (RR: 1.92; 95% CI: 0.66 to 5.60; one RCT (33) ). + +- Subgroup analyses revealed no difference in the effect for CLABSI based on age (adults versus children) or setting (ICU versus general ward). + +## Evidence-to-decision + +A potentially reduced equity was noted due to the different availability of products around the world and their moderate costs, in particular when considering LMICs, but the intervention was considered probably cost-effective. No issues were identified in acceptability and feasibility. + +## Implementation considerations + +- The recommendation refers to using a chlorhexidine-containing body wash (liquid or impregnated wipes) daily and not immediately prior to line insertion. The GDG acknowledges that there are variations in the available protocols on body washing and directs health and care workers to follow their national and local policies. +- The recommendation refers to all critically-ill patients that require a CVC and not limited to the ICU. +- It is advisable to engage nursing and support staff as key stakeholders in the decision (that is, time required for bathing). +- It is also advisable to engage patients and their families, considering the potential adverse effects on the skin related to exposure to chlorhexidine, including asking for any known intolerance and rare allergic reactions to chlorhexidine. +- WASH services and standards (64, 65) are essential to enable critical IPC practices, including this recommendation on body wash. + +## Research needs + +- There is a significant variation in available protocols on how to perform patient bathing. The GDG identified this as an area of research interest to determine the most effective protocol and product to be used (that is, liquid wash versus wipes or other means, rinsing versus no rinsing, which solution to use). +- The GDG also identified the need for additional research on the use of antiseptic products other than chlorhexidine (that is, octenidine and others) using multicentre RCTs or other types of trials (that is, adaptive) and focusing on specific populations (such as haematology patients or the paediatric ICU). +- AMR and other wider implications (that is, impact on skin microbiome, cross-resistance to antibiotics and on the epidemiology of other infections caused by gram-positive and gramnegative bacteria) associated with the use of chlorhexidine and other body wash products were identified as important areas for research. +- Cost-benefit research studies including baseline surveillance data to define potential thresholds for universal use were also considered as other areas for further research. + +## 3.3 Insertion + +## 3.3.1 Insertion pack/kit + +- Good practice statement 6. WHO recommends that clinicians use a standardized insertion pack/kit when placing a CVC in adults, adolescents, children and neonates (Good practice statement) + +## 3.3.2 CVC insertion by an insertion team + +- WHO makes no recommendation regarding the use of a dedicated CVC insertion teams in adults, adolescents, children, or neonates, as the evidence remains inconclusive. + +## Remarks + +- A CVC insertion team is defined as consisting of individuals specifically trained and competent in CVC insertion who are dedicated to perform the insertion of CVCs. +- The search criteria used in the systematic review were inclusive as possible, including terms such as ' insertion team ', ' vascular access team ', intravenous therapy team '. +- Establishing a dedicated CVC insertion team is an intervention that is different from ensuring specific training for all those tasked with CVC insertion, which is covered by good practice statements 1 to 3 in these guidelines. +- Consideration should also be given to specific populations (i.e., neonates, children, or patients with known difficult intravenous access) as the potential benefit in preventing CLABSI may be confined to these groups. +- The GDG members acknowledged the difficulties in designing a RCT to evaluate this topic and the very limited available evidence. + +## Rationale for the decision + +Based on the evidence provided (two uncontrolled before-after studies and no RCTs), the GDG considered both the desirable and undesirable effects to be small. The GDG judged that the crucial factor was the adequate training of the clinician inserting the CVC, rather than having a dedicated team itself. For this reason, the GDG considered that the balance of effects did not favour either the intervention (a formal insertion team) or the comparison (insertion by a clinician who is not part of a formal insertion team), provided that the clinician has undergone appropriate training and demonstrated competency in CVC insertion. Another concern expressed by the GDG was the potential loss of knowledge and skills in CVC insertion among non-team members (doctors and nurses), such that their insertion competency could decline. This may be especially impactful in emergency situations where they are required to urgently insert a CVC without the assistance of a formal insertion team, with potential implications affecting the wider hospital capacity and patient care. Overall, given the very low certainty of the evidence, no recommendation could be made. + +## Summary of the evidence + +- The Systematic Reviews Expert Group did not identify any RCTs on the topic, but only two uncontrolled before-after studies (66, 67) evaluating the use of a dedicated CVC insertion (for non-haemodialysis) team compared with not using a dedicated CVC insertion team. The risk of bias in both studies was rated as high due to their uncontrolled design (no formal assessment). +- There was very low certainty of evidence from one study in children and adults reporting a 58% reduction in the number of CLABSIs after the introduction of a highly specialized vascular access team (67) . Similarly, there was very low certainty of evidence from another study in neonates reporting that overall CLABSI rates decreased by 65% after implementation of the line team (66) . +- There were no studies identified reporting on catheter-related mortality, all-cause mortality, sepsis pneumothorax, local site infections, bleeding events that require action, cardiac tamponade, deep vein thrombosis or venous stenosis. + +## Evidence-to-decision + +Increased moderate costs (due to the resources required to maintain a dedicated team), the probably reduced equity, variable acceptability by health care workers and patients (hospital management might not be in favour due to the additional costs, but patient satisfaction is likely to be improved) and low feasibility (as having a dedicated team is not always possible due to staff shortages) were all considered, resulting in a decision to make no recommendation.. The overall cost-effectiveness judgement did not favour either the intervention or the comparison. + +## Research needs + +- Further research is needed to compare the potential cost-benefit of using a formal CVC insertion team versus an educational/behavioural programme for clinicians inserting CVC, including both ICU and non-ICU settings. + +## 3.3.3 Sterile technique + +- Good practice statement 7. WHO recommends using a sterile technique for the insertion of all CVCs in adults, adolescents, children and neonates. (Good practice statement) +- Good practice statement 8. WHO recommends that clinicians use sterile single-use gloves compared to non-sterile gloves when inserting a CVC in adults, adolescents, children and neonates. + +(Good practice statement) + +- Recommendation 2. WHO suggests using a sterile technique involving maximal sterile barrier precautions over a sterile technique not involving maximal sterile barrier precautions at the time of CVC insertion in adults, adolescents, children and neonates. + +(Conditional recommendation, very low certainty of evidence) + +## Remarks + +- Maximal sterile barrier precautions: sterile barrier precautions that include the use of a cap, mask, sterile gown, sterile gloves and a sterile full body drape (11) . +- Sterile technique is defined as a set of specific practices and procedures performed to make equipment and areas free from all microorganisms and to maintain that sterility (11) . +- GDG members acknowledged that the above definition of sterile technique as comparator also seems to be generic and it may not provide enough practical details. + +## Rationale for the recommendation + +There was an extensive discussion during which a number of GDG members expressed the opinion that a strong recommendation would have been more suitable; others suggested a conversion into a good practice statement. However, it was decided to assess the available evidence and to proceed with the evidence-to-decision framework. Following the assessment, the GDG judged the desirable and undesirable effects to be small and trivial, respectively, but with a balance of effects probably favouring the intervention, despite the very low certainty of evidence. In view of the data presented, the GDG members opted for a conditional recommendation in favour of maximal sterile barrier precautions, but acknowledging that the current evidence is weak and more studies are needed to assess if less barriers may be sufficient. + +## Summary of the evidence + +The Systematic Reviews Expert Group identified eight studies (two RCTs (68, 69) and six NRSIs (70-75) ) comparing maximal sterile barrier precautions in adults, children and adolescents, and neonates. + +- There was very low certainty of evidence that maximal sterile barrier precautions may result in fewer CLABSIs than a lesser standard of precautions (RR: 0.47, 95% CI: 0.10 to 2.22; two RCTs (68, 69) ). +- Two non-randomized studies also reported very low certainty of evidence that maximal sterile barrier precautions may result in fewer CLABSIs than a lesser standard of precautions (RR: 0.21; 95% CI: 0.05 to 0.94; two non-RCTs (70, 71) ) +- There was very low certainty of evidence that maximal sterile barrier precautions may result in little to no difference in local insertion site infections when compared with a lesser standard of precautions (RR: 1.01; 95% CI: 0.06 to 16.03; one RCT (68) ). +- There were no studies identified that reported on catheter-related mortality, all-cause mortality, sepsis and other complications. + +## Evidence-to-decision + +The intervention may increase costs due to the additional equipment required and it is probably accepted and feasible as it is already common practice. However, patients may have more discomfort with full body drapes. In addition, the GDG judged equity to be probably increased. + +## Implementation considerations + +- Ensure adequate training, understanding and competency in the application of maximal sterile barriers precautions. +- The GDG discussed the need for a dedicated procedure room for line insertion and noted that this is not practical for critically-ill patients and may be an issue in some health care facilities, particularly in LMICs. Furthermore, it is not part of the current definition of maximal sterile barrier precautions. + +## Research needs + +- More research studies are needed to assess if lesser sterile precautions are needed, with a trial design and platform (for example, adaptive (76, 77) ) that would allow to clearly distinguish the impact of the different components within maximal sterile barrier precautions (that is, cap, mask, full body drape, the environment where the line is placed) and allow to answer multiple questions simultaneously. + +## 3.3.4 Skin disinfection + +- Good practice statement 9. WHO recommends that skin disinfection should always be used prior to the insertion of all CVCs in adults, adolescents, children and neonates. (Good practice statement) +- Recommendation 3. WHO suggests using an alcohol-based formulation over an aqueous-based antiseptic formulation for skin disinfection before CVC insertion in adults, adolescents, children, and neonates. + +(Conditional recommendation, low certainty of evidence) + +## Remarks + +- Alcohol-based antiseptics should be the preferred choice for skin disinfection before CVC insertion. +- It was acknowledged that alcohol-based formulations can cause skin irritation, dryness and a risk of pain in case of laceration and these potential side-effects should be taken into consideration when using these products. Some of these side-effects may be caused by either the alcohol or the antiseptic component. +- Alcohol-based antiseptics can cause skin lesions in preterm infants without intact skin. + +## Rationale for the recommendation + +The GDG considered alcohol-based formulations as the preferred option for skin disinfection over aqueous formulations, with a conditional recommendation due to the low certainty of evidence. The GDG considered the desirable effects of alcohol-based formulations for skin disinfection to be moderate and the undesirable effects trivial, with a balance of effects probably favouring the intervention. + +## Summary of the evidence + +The Systematic Reviews Expert Group found data from five RCTs (78-82) . + +- There was low certainty of evidence that alcohol-based solutions may result in fewer CLABSIs than aqueous-based solutions for skin disinfection (RR: 0.59; 95% CI: 0.36 to 0.98; five RCTs (78-82) ). +- There was very low certainty of evidence that alcohol-based solutions may result in less allcause mortality than aqueous-based solutions for skin disinfection (RR: 0.79; 95% CI: 0.48 to 1.30; two RCTs (78, 79) ). +- There was very low certainty of evidence that alcohol-based solutions may result in fewer sepsis episodes when compared with aqueous-based solutions for skin disinfection (RR: 0.68; 95% CI: 0.35 to 1.30; one RCT (78) ). +- There were no studies identified that reported on catheter-related mortality, pneumothorax, local insertion site infections and other complications. \ No newline at end of file diff --git a/datasets/test/fixtures/pdf/who_9789240121805_excerpt.pdf b/datasets/test/fixtures/pdf/who_9789240121805_excerpt.pdf new file mode 100644 index 00000000..649cb7fc Binary files /dev/null and b/datasets/test/fixtures/pdf/who_9789240121805_excerpt.pdf differ diff --git a/datasets/test/fixtures/pdf/who_9789240124233_excerpt.expected.md b/datasets/test/fixtures/pdf/who_9789240124233_excerpt.expected.md new file mode 100644 index 00000000..a21d551c --- /dev/null +++ b/datasets/test/fixtures/pdf/who_9789240124233_excerpt.expected.md @@ -0,0 +1,141 @@ +Table 1: HIV service delivery recommendations + +| Date* | Recommendations | Status | +|-------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------| +| Linkage and ART initiation | Linkage and ART initiation | Linkage and ART initiation | +| 2016 | Following an HIV diagnosis, a package of support interventions should be offered to ensure timely linkage to care for all people living with HIV (Strong recommendation, moderate-certainty evidence) . | Revalidated | +| 2021 | Health systems should invest in people-centred practices and communication, including ongoing training, mentoring, supportive supervision and monitoring of health workers, to improve the relationships between clients and health-care providers (Good practice statement) . | Revalidated | +| 2019 | ART initiation should follow the overarching principles of providing people-centred care. People-centred care should be focused and organized around the health needs, preferences and expectations of people and communities, upholding individual dignity and respect, especially for vulnerable populations (Good practice statement) . | Revalidated | +| 2021 | Antiretroviral therapy (ART) initiation may be offered outside the health facility (Conditional recommendation, low- to moderate-certainty evidence ). | Revalidated | +| 2017 | Rapid ART initiation should be offered to all people living with HIV following a confirmed HIV diagnosis and clinical assessment (Strong recommendation: high- certainty evidence for adults, low-certainty evidence for children) | Revalidated | +| 2021 | The offer of same-day ART initiation should include approaches to improve uptake, treatment adherence and retention such as tailored client education, counselling and support (Good practice statement) . | Revalidated | +| Clinical visits and medication pick-up | Clinical visits and medication pick-up | Clinical visits and medication pick-up | +| 2021 | People established on ART should be offered clinical visits every 3-6 months, preferably every six months if feasible (Strong recommendation, moderate-certainty evidence ). | Revalidated | +| 2021 | People established on ART should be offered refills of ART lasting 3-6 months, preferably six months if feasible (Strong recommendation, moderate-certainty evidence). | Revalidated | +| Adherence and engagement in care | Adherence and engagement in care | Adherence and engagement in care | +| 2025 | Adherence support interventions should be provided to people on ART (Strong recommendation, moderate-certainty evidence) . | Updated | +| 2021 | Viral load for treatment monitoring should be complemented with non-judgemental, tailored approaches to assessing adherence (Good practice statement) . | Revalidated | +| 2021 | HIV programmes should implement interventions to trace people who have disengaged from care and provide support for re-engagement (Strong recommendation, low-certainty evidence) . | Revalidated | +| Services for adolescents and young people | Services for adolescents and young people | Services for adolescents and young people | +| 2021 | Psychosocial interventions should be provided to all adolescents and young adults living with HIV (Strong recommendation, moderate-certainty evidence) . | Revalidated | +| 2013 | Adolescent-friendly services should be implemented in HIV services to ensure engagement and improved outcomes (Strong recommendation, moderate-certainty evidence) . | Revalidated | + +Table 1: HIV service delivery recommendations (cont'd) + +| Date* | Recommendations | Status | +|-------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------| +| Services for adolescents and young people | Services for adolescents and young people | Services for adolescents and young people | +| 2013 | Adolescents should be counselled about the potential benefits and risks of disclosing their HIV status to others and empowered and supported to determine whether, when, how and to whom to disclose (Conditional recommendation, very-low -certainty evidence) . | Revalidated | +| Task sharing | Task sharing | Task sharing | +| 2016 | Trained non-physician clinicians, midwives and nurses can initiate first-line ART (Strong recommendation, moderate-certainty evidence) . | Revalidated | +| 2016 | Trained non-physician clinicians, midwives and nurses can maintain ART (Strong recommendation, moderate-certainty evidence) . | Revalidated | +| 2016 | Trained and supervised community health workers can dispense ART between regular clinical visits (Strong recommendation, moderate-certainty evidence) . | Revalidated | +| 2016 | Trained and supervised lay health-care providers can distribute ART (Strong recommendation, low-certainty evidence) . | Revalidated | +| 2021 | Task sharing of specimen collection and point-of-care testing with non-laboratory personnel should be implemented when professional staffing capacity is limited (Strong recommendation, moderate-certainty evidence) . | Revalidated | +| Service Delivery models and integration | Service Delivery models and integration | Service Delivery models and integration | +| 2013 | Decentralization of ART care should be considered as a way to increase access and improve retention in care (Strong recommendation, moderate-to-low-certainty evidence) . | Revalidated | +| 2013 | In generalized epidemic settings, ART should be initiated and maintained in pregnant and postpartum women and in infants at maternal and child health-care settings, with linkage and referral to ongoing HIV care and ART, if appropriate (Strong recommendation, low-certainty evidence) . | Revalidated | +| 2021 | Sexual and reproductive health services, including contraception, may be integrated with HIV services (Conditional recommendation, very-low-certainty evidence) . | Revalidated | +| 2013 | In settings with a high burden of HIV and tuberculosis (TB), ART should be initiated in TB treatment settings, with linkage to ongoing HIV care and ART (Strong recommendation, very-low-certainty evidence) . | Revalidated | +| 2013 | In settings with a high burden of HIV and TB, TB treatment may be provided for people living with HIV in HIV care settings if they have been diagnosed with TB (Strong recommendation, very-low-certainty evidence) . | Revalidated | +| 2025 | Diabetes and hypertension care should be integrated with HIV services (Strong recommendation, moderate-to-very-low-certainty evidence) . | Updated | +| 2025 | Mental health care for depression, anxiety and alcohol use disorders should be integrated with HIV services (Strong recommendation, moderate-to-very-low-certainty evidence) . | New | + +## 1. Introduction + +HIV remains a major public health challenge and a leading cause of illness and death in many low- and middleincome countries, despite the wide availability of effective antiretroviral therapy and proven prevention tools. + +In many settings, evidence-informed interventions for HIV prevention, testing, treatment and long-term care are not fully implemented, delivered inconsistently or reach people too late, contributing to ongoing transmission, advanced disease and avoidable mortality. Persistent health system constraints - including workforce shortages, weak supply chains and limited integration with related services such as those for noncommunicable diseases and mental health care - further hinder effective service delivery. + +These HIV service delivery guidelines provide updated and consolidated recommendations to support countries, programme managers, health-care workers, communities and other stakeholders to organize services that are people-centred, integrated, equitable and grounded in the best available evidence. The guidelines aim to improve access to and continuity of high-quality HIV services, reduce inequities in outcomes and accelerate progress towards ending AIDS as a public health threat. + +## 2. Linkage and ART initiation + +## 2.1 Linkage from HIV testing to enrolment in care + +## Recommendation + +Following an HIV diagnosis, a package of support interventions should be offered to ensure timely linkage to care for all people living with HIV. + +(Strong recommendation, moderate-certainty evidence) + +The following interventions have demonstrated benefit in improving linkage to care following an HIV diagnosis: + +- streamlined interventions to reduce time between diagnosis and engagement in care, including (i) enhanced linkage with case management; (ii) support for HIV disclosure; (iii) tracing; (iv) training staff to provide multiple services; and (v) streamlined services (moderate-certainty evidence) ; +- peer support a and navigation approaches for linkage (moderate-certainty evidence) ; and +- quality improvement approaches using data to improve linkage (low-certainty evidence) . + +a Includes peer counselling. + +## Good practice statements + +ART initiation should follow the overarching principles of providing people-centred care. People-centred care is care that is focused and organized around the health needs, preferences and expectations of people and communities, upholding individual dignity and respect, especially for vulnerable populations. It should promote the engagement and support of people and families to play an active role in their own care through informed decision-making. + +All people newly diagnosed with HIV should be retested to verify their HIV status before starting ART, using the same testing strategy and algorithm as the initial test. To minimize the risk of misdiagnosis, this approach should be maintained in settings in which rapid ART initiation is being implemented. + +Revalidated + + + +## Background + +Linkage to HIV prevention, treatment and care after testing remains a challenge, with disproportionate gaps for key populations, men, young people and previously diagnosed people living with HIV (not receiving ART, disengaged or lost to care). + +HIV testing service providers are primarily responsible for linkage to care. People testing HIV positive should be assessed for advanced HIV disease using CD4 cell count testing and offered ART, and those testing negative should be linked to prevention services. + +## Rationale + +Evidence-informed interventions to support linkage can be classified into three approaches (2) : + +- streamlined services via enhanced linkage with case management, HIV disclosure support, client tracing for non-engagers and staff training for multiple services; +- peer support and navigation interventions, including home visits, system navigation and enhanced counselling; and +- quality improvement interventions enhance linkage to care (3) . + +## Implementation considerations + +- Interventions may vary based on the context, including health-care delivery systems, geography and target population. +- A combination of interventions may be needed to improve linkage for specific underserved groups, especially key populations and men. +- Barriers to linkage to HIV care and ART initiation should be assessed and addressed, especially for populations facing multiple structural and individual barriers. +- Linkage for children can be improved using point-of-care early infant diagnosis, SMS/GSM/GPRS printers to accelerate access to laboratory results and family-centred models delivering care to mother, baby, and partner at the same point. +- Health facilities should have capacity to provide services for key populations. Community- and peer-based approaches can be especially effective in restrictive legal settings. + +WHO guidelines on HIV testing services (4) provide information on post-test services and linkage to care. + +## 2.2 People-centred care + +## Good practice statement + +Health systems should invest in people-centred practices and communication, including ongoing training, mentoring, supportive supervision and monitoring of health workers, to improve the relationships between clients and health-care providers. + +## HIV programmes should: + +- provide people-centred care that is focused and organized around the health needs, preferences and expectations of people and communities, upholding individual dignity and respect, especially for underserved populations, and engage and support people and families to play an active role in their own care by informed decision-making; +- offer safe, acceptable and appropriate clinical and non-clinical services in a timely fashion, aiming to reduce morbidity and mortality associated with HIV infection and to improve health outcomes and quality of life in general; and +- promote the efficient and effective use of resources. + +Revalidated + +## Background + +People-centred health services are an approach to care that consciously adopts the perspectives of individuals, families and communities and sees them as participants and beneficiaries of trusted health systems that respond to their needs and preferences in humane and holistic ways. This approach acknowledges the experiences and perspectives of health-care providers that may enable or prevent the delivery of high-quality people-centred care. + +## Rationale + +- A systematic review (5) identified several interventions to enhance people-centred care for people living with HIV. Overall, studies reported beneficial effects of these approaches across the HIV cascade outcomes, including improved ART uptake, adherence and viral load suppression. +- Studies have shown that people are willing to travel longer distances to be seen by a health-care provider with a respectful and caring attitude, and negative health-care worker attitudes contribute to loss to care and poor programme outcomes (6) . + +Interventions found to improve relationships between clients and health-care providers can be classified into the following approaches: + +- providing friendly and welcoming services: training providers to make general HIV services more welcoming, including for clients who have disengaged from care; +- conducting sensitization training for clinical and non-clinical health-care providers to improve care for key populations both at the primary care and community levels; such training should include issues related to stigma and discrimination; +- offering individualized adherence counselling and person-centred communication such as shared decisionmaking and planning for ART initiation and adherence; +- facilitating client education in empowerment and communication skills; and +- providing feedback to health-care workers on client concerns and evaluation of service quality such as community score cards and client feedback mechanisms combined with quality improvement exercises. + +## Implementation considerations + +- Build capacity for ongoing training, mentoring and supportive supervision on people-centred communication, stigma reduction and welcoming services. +- Integrate sensitization training for all staff (clinical and non-clinical) on respectful attitudes, stigma and discrimination, re-engagement of clients who have disengaged, and support for women and other vulnerable groups experiencing violence or sexual health concerns. +- Establish routine client feedback mechanisms (such as satisfaction questionnaires, community score cards and suggestion boxes) and use the results in facility quality-improvement meetings. +- Involve clients and community representatives in designing and reviewing services. +- Review workload, staffing and client flow to allow time for person-centred interactions. \ No newline at end of file diff --git a/datasets/test/fixtures/pdf/who_9789240124233_excerpt.pdf b/datasets/test/fixtures/pdf/who_9789240124233_excerpt.pdf new file mode 100644 index 00000000..bf25b8b5 Binary files /dev/null and b/datasets/test/fixtures/pdf/who_9789240124233_excerpt.pdf differ diff --git a/datasets/test/fixtures/who_listing_api.json b/datasets/test/fixtures/who_listing_api.json new file mode 100644 index 00000000..a4392d3b --- /dev/null +++ b/datasets/test/fixtures/who_listing_api.json @@ -0,0 +1,20 @@ +{ + "@odata.context": "https://www.who.int/api/hubs/$metadata#publications(Title,ItemDefaultUrl,FormatedDate,Tag,DownloadUrl)", + "@odata.count": 356, + "value": [ + { + "ItemDefaultUrl": "/9789240121805", + "Title": "Guidelines for the prevention of bloodstream infections and other infections associated with the use of intravascular catheters: part 2: central venous catheters", + "FormatedDate": "28 May 2026", + "Tag": "Guideline", + "DownloadUrl": "https://iris.who.int/server/api/core/bitstreams/f750f24d-c0c2-425c-85fd-ec310d2ce994/content" + }, + { + "ItemDefaultUrl": "/9789240121744", + "Title": "WHO guideline for screening and treatment of cervical pre-cancer lesions for cervical cancer prevention", + "FormatedDate": "8 May 2026", + "Tag": "Guideline", + "DownloadUrl": "https://iris.who.int/server/api/core/bitstreams/32214b73-0e95-4243-9e83-617948510dcd/content" + } + ] +} diff --git a/datasets/test/fixtures/who_publication_overview.html b/datasets/test/fixtures/who_publication_overview.html new file mode 100644 index 00000000..b6f16f29 --- /dev/null +++ b/datasets/test/fixtures/who_publication_overview.html @@ -0,0 +1,17 @@ + +
+

Guidelines for the prevention of bloodstream infections and other infections associated with the use of intravascular catheters: part 2: central venous catheters

+
+
28 May 2026
+
 | Guideline
+
+
+ Download (1.2 MB) +

Overview

+

These WHO guidelines provide evidence-based recommendations for the prevention of bloodstream infections (BSIs) and other infections associated with the use of central venous catheters (CVCs) across health care settings.

+

WHO Team

+

Infection Prevention and Control (IPC)

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ISBN: 978-92-4-012180-5

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+
+ diff --git a/datasets/test/test_scraping_pdf.py b/datasets/test/test_scraping_pdf.py new file mode 100644 index 00000000..2c7173f5 --- /dev/null +++ b/datasets/test/test_scraping_pdf.py @@ -0,0 +1,102 @@ +"""Tests for PDF-to-markdown conversion helpers.""" + +import pytest + +from amfv_datasets.scraping.pdf import ( + PdfBackend, + PdfConversionError, + count_markdown_sections, + pdf_to_markdown, +) +from amfv_datasets.scraping.pdf import _strip_running_header as strip_running_header + +_GUIDELINE_TITLE = "Guidelines for the prevention of bloodstream infections" + + +@pytest.mark.parametrize( + ("markdown", "expected"), + [ + pytest.param("## A\ntext\n## B\n### sub\n## C", 3, id="counts-shallowest-level"), + pytest.param("# Title\n## A\n## B", 1, id="ignores-deeper-levels"), + pytest.param("no headings at all", 1, id="unstructured-counts-as-one"), + pytest.param("", 1, id="empty-counts-as-one"), + ], +) +def test_count_markdown_sections(markdown: str, expected: int) -> None: + """Sections are counted from the shallowest heading level present.""" + assert count_markdown_sections(markdown) == expected + + +def test_strip_running_header_removes_repeated_title() -> None: + """Repeated page headers matching the title are dropped.""" + markdown = f"{_GUIDELINE_TITLE}\n\n## Recommendations\n\nUse aseptic technique.\n\n{_GUIDELINE_TITLE}\n\nMore text." + + cleaned = strip_running_header(markdown, _GUIDELINE_TITLE) + + assert _GUIDELINE_TITLE not in cleaned + assert "## Recommendations" in cleaned + assert "Use aseptic technique." in cleaned + assert "More text." in cleaned + + +def test_strip_running_header_removes_shortened_title() -> None: + """Publishers shorten the title in page headers, so prefixes are dropped.""" + short = "Guidelines for the prevention of bloodstream infections" + full = f"{short} associated with the use of intravascular catheters: part 2" + markdown = f"{short}\n\n## Recommendations\n\nUse aseptic technique." + + cleaned = strip_running_header(markdown, full) + + assert short not in cleaned + assert "Use aseptic technique." in cleaned + + +def test_strip_running_header_removes_doubled_header_line() -> None: + """Left and right page headers merged onto one line are still dropped.""" + markdown = f"{_GUIDELINE_TITLE} {_GUIDELINE_TITLE}\n\nUse aseptic technique." + + cleaned = strip_running_header(markdown, _GUIDELINE_TITLE) + + assert "Guidelines for the prevention" not in cleaned + assert "Use aseptic technique." in cleaned + + +def test_strip_running_header_keeps_short_title_fragments() -> None: + """A short word that merely starts the title is content, not a header.""" + markdown = "Guidelines\n\nUse aseptic technique." + + cleaned = strip_running_header(markdown, _GUIDELINE_TITLE) + + assert "Guidelines" in cleaned + + +def test_strip_running_header_keeps_repeated_guideline_content() -> None: + """GRADE qualifiers repeat legitimately and must survive header stripping.""" + qualifier = "(Strong recommendation, moderate-certainty evidence)" + markdown = f"## One\n\n{qualifier}\n\n## Two\n\n{qualifier}\n\n## Three\n\n{qualifier}" + + cleaned = strip_running_header(markdown, _GUIDELINE_TITLE) + + assert cleaned.count(qualifier) == 3 + + +def test_strip_running_header_without_header_only_trims() -> None: + """Passing no header leaves the markdown untouched apart from trimming.""" + assert strip_running_header("\n\n## Kept\n\n", None) == "## Kept" + + +def test_pdf_to_markdown_rejects_empty_payload() -> None: + """An empty payload is a conversion error rather than an empty document.""" + with pytest.raises(PdfConversionError, match="empty PDF payload"): + pdf_to_markdown(b"") + + +def test_pdf_to_markdown_rejects_unknown_backend() -> None: + """Only registered backends are accepted.""" + with pytest.raises(PdfConversionError, match="Unsupported PDF backend"): + pdf_to_markdown(b"%PDF-1.7", backend="marker") # type: ignore[arg-type] + + +def test_pdf_backend_values() -> None: + """The backend enum serializes to a stable metadata string.""" + assert PdfBackend.DOCLING.value == "docling" diff --git a/datasets/test/test_scraping_pdf_fixtures.py b/datasets/test/test_scraping_pdf_fixtures.py new file mode 100644 index 00000000..f4f6c2dd --- /dev/null +++ b/datasets/test/test_scraping_pdf_fixtures.py @@ -0,0 +1,160 @@ +"""Conversion tests against real WHO guideline PDF excerpts. + +These run the actual Docling pipeline rather than a stub, so they are the check +that guideline content survives conversion. They need the `pdf` extra +(`uv sync --group pdf`) and are skipped when it is absent, which is why CI stays +green without installing a PDF stack. + +Assertions here are deliberately semantic: they check that a recommendation, its +certainty rating and its table rows are present, not that the markdown is +byte-for-byte identical. A Docling upgrade may reflow whitespace without +changing meaning, and that must not fail the suite. + +The byte-exact comparison against the committed `*.expected.md` files is opt-in +via `AMFV_CHECK_GOLDEN=1`; see `datasets/benchmarks/README.md`. + +The fixture PDFs are page excerpts of WHO guidelines redistributed under +CC BY-NC-SA 3.0 IGO; see `amfv_datasets/scraping/LICENSE_NOTES.md`. +""" + +import os +from functools import cache +from pathlib import Path + +import httpx +import pytest + +from amfv_datasets.scraping.pdf import HAS_DOCLING, count_markdown_sections, pdf_to_markdown +from amfv_datasets.scraping.who import WhoPublicationRef, scrape_publication + +pytestmark = pytest.mark.skipif(not HAS_DOCLING, reason="requires the `pdf` extra (uv sync --group pdf)") + +_FIXTURES = Path(__file__).parent / "fixtures" +_PDF_FIXTURES = _FIXTURES / "pdf" + +_CVC_PDF = "who_9789240121805_excerpt.pdf" +_CVC_TITLE = ( + "Guidelines for the prevention of bloodstream infections and other infections " + "associated with the use of intravascular catheters: part 2: central venous catheters" +) +_HIV_PDF = "who_9789240124233_excerpt.pdf" +_HIV_TITLE = "Consolidated HIV guidelines: service delivery" + +_PAGE_URL = "https://www.who.int/publications/i/item/9789240121805" +_DOWNLOAD_URL = "https://iris.who.int/server/api/core/bitstreams/f750f24d-c0c2-425c-85fd-ec310d2ce994/content" + +_CHECK_GOLDEN_ENV = "AMFV_CHECK_GOLDEN" +_UPDATE_GOLDEN_ENV = "AMFV_UPDATE_GOLDEN" +_FIXTURE_DOCUMENTS = [ + pytest.param(_CVC_PDF, _CVC_TITLE, id="bloodstream-infections"), + pytest.param(_HIV_PDF, _HIV_TITLE, id="hiv-service-delivery"), +] + + +@cache +def _converted(pdf_name: str, title: str) -> str: + """Convert a fixture PDF once and reuse it across assertions.""" + return pdf_to_markdown((_PDF_FIXTURES / pdf_name).read_bytes(), running_header=title, name=pdf_name) + + +def _table_rows(markdown: str) -> int: + """Count markdown table rows.""" + return sum(1 for line in markdown.splitlines() if line.strip().startswith("|")) + + +def test_recommendation_and_grade_certainty_survive_conversion() -> None: + """The recommendation text and its certainty rating both reach the markdown.""" + markdown = _converted(_CVC_PDF, _CVC_TITLE) + + assert "Recommendation 1." in markdown + assert "chlorhexidine-containing body wash" in markdown + assert "certainty of evidence" in markdown + assert "## Remarks" in markdown + assert "## Summary of the evidence" in markdown + + +def test_heading_structure_is_recovered() -> None: + """Section structure is preserved so documents can be chunked later.""" + markdown = _converted(_CVC_PDF, _CVC_TITLE) + + assert count_markdown_sections(markdown) >= 15 + + +def test_running_header_is_removed_from_real_pdf() -> None: + """The repeated page header does not leak into the document body.""" + markdown = _converted(_CVC_PDF, _CVC_TITLE) + + header_lines = [ + line + for line in markdown.splitlines() + if line.strip().casefold().startswith("guidelines for the prevention of bloodstream") + ] + assert header_lines == [] + + +def test_recommendation_table_structure_is_preserved() -> None: + """Recommendation tables convert to markdown tables with their rows intact. + + Row loss here is the failure mode that makes a table unusable for fact + verification, so the row count is asserted rather than mere table presence. + """ + markdown = _converted(_HIV_PDF, _HIV_TITLE) + + assert "Table 1: HIV service delivery recommendations" in markdown + assert "| Date" in markdown + assert _table_rows(markdown) >= 30 + assert "Rapid ART initiation should be offered" in markdown + + +@pytest.mark.skipif( + not (os.environ.get(_CHECK_GOLDEN_ENV) or os.environ.get(_UPDATE_GOLDEN_ENV)), + reason=f"set {_CHECK_GOLDEN_ENV}=1 to diff against the committed .expected.md files", +) +@pytest.mark.parametrize(("pdf_name", "title"), _FIXTURE_DOCUMENTS) +def test_conversion_matches_golden_output(pdf_name: str, title: str) -> None: + """Compare conversion byte for byte against the committed markdown. + + Opt-in because it is sensitive to the Docling version: an upgrade that + reflows whitespace should prompt a human to review the new output, not break + CI for everyone. + """ + markdown = _converted(pdf_name, title) + golden = _PDF_FIXTURES / f"{Path(pdf_name).stem}.expected.md" + + if os.environ.get(_UPDATE_GOLDEN_ENV): + golden.write_text(markdown, encoding="utf-8") + pytest.skip(f"rewrote {golden.name}") + + regenerate = f"{_UPDATE_GOLDEN_ENV}=1 uv run --group pdf pytest {Path(__file__).name}" + assert markdown == golden.read_text(encoding="utf-8"), ( + f"Conversion of {pdf_name} no longer matches {golden.name}. " + f"Review the difference, then regenerate with `{regenerate}`." + ) + + +def test_scrape_publication_emits_full_text_document() -> None: + """End to end: landing page plus real PDF become one full-text document.""" + html = (_FIXTURES / "who_publication_overview.html").read_text(encoding="utf-8") + pdf_bytes = (_PDF_FIXTURES / _CVC_PDF).read_bytes() + + def handler(request: httpx.Request) -> httpx.Response: + if str(request.url) == _PAGE_URL: + return httpx.Response(200, text=html) + return httpx.Response(200, content=pdf_bytes) + + ref = WhoPublicationRef( + publication_id="9789240121805", + title=_CVC_TITLE, + page_url=_PAGE_URL, + download_url=_DOWNLOAD_URL, + ) + + document = scrape_publication(httpx.Client(transport=httpx.MockTransport(handler)), ref) + + assert document.metadata["content_scope"] == "full" + assert document.metadata["pdf_backend"] == "docling" + assert document.metadata["pdf_bytes"] == len(pdf_bytes) + assert document.section_count >= 15 + assert "### Overview" in document.content + assert "central venous catheters (CVCs)" in document.content + assert "chlorhexidine-containing body wash" in document.content diff --git a/datasets/test/test_scraping_who.py b/datasets/test/test_scraping_who.py new file mode 100644 index 00000000..018bdfba --- /dev/null +++ b/datasets/test/test_scraping_who.py @@ -0,0 +1,229 @@ +"""Tests for WHO scraping helpers.""" + +import json +from pathlib import Path + +import httpx +import pytest + +from amfv_datasets.scraping.html import LinkMode +from amfv_datasets.scraping.pdf import PdfConversionError +from amfv_datasets.scraping.who import ( + BASE_URL, + WHO_LICENSE, + WhoFetchError, + WhoListingPage, + WhoPublicationRef, + build_publication_text, + list_publications, + publication_ref_from_url, + scrape_publication, +) + +_FIXTURES = Path(__file__).parent / "fixtures" +_CVC_GUIDELINE_TITLE = ( + "Guidelines for the prevention of bloodstream infections and other infections " + "associated with the use of intravascular catheters: part 2: central venous catheters" +) +_CERVICAL_GUIDELINE_TITLE = ( + "WHO guideline for screening and treatment of cervical pre-cancer lesions for cervical cancer prevention" +) +_PAGE_URL = "https://www.who.int/publications/i/item/9789240121805" +_DOWNLOAD_URL = "https://iris.who.int/server/api/core/bitstreams/f750f24d-c0c2-425c-85fd-ec310d2ce994/content" +_PDF_BYTES = b"%PDF-1.7 fake guideline payload" +_PDF_MARKDOWN = "## Recommendations\n\nUse aseptic technique.\n\n## Evidence\n\n### Certainty\n\nModerate." + + +def _publication_ref(*, download_url: str | None = _DOWNLOAD_URL) -> WhoPublicationRef: + """Build a CVC guideline ref pointing at the fixture page.""" + return WhoPublicationRef( + publication_id="9789240121805", + title=_CVC_GUIDELINE_TITLE, + page_url=_PAGE_URL, + publication_date="28 May 2026", + tag="Guideline", + download_url=download_url, + ) + + +def _page_and_pdf_client(*, pdf_status: int = 200) -> httpx.Client: + """Serve the fixture landing page and a stub PDF payload.""" + html = (_FIXTURES / "who_publication_overview.html").read_text(encoding="utf-8") + + def handler(request: httpx.Request) -> httpx.Response: + if str(request.url) == _PAGE_URL: + return httpx.Response(200, text=html) + assert str(request.url) == _DOWNLOAD_URL + return httpx.Response(pdf_status, content=_PDF_BYTES) + + return httpx.Client(transport=httpx.MockTransport(handler)) + + +def _fake_converter(data: bytes, title: str, publication_id: str) -> str: + """Stand in for Docling so tests stay offline and fast.""" + assert data == _PDF_BYTES + assert title == _CVC_GUIDELINE_TITLE + assert publication_id == "9789240121805" + return _PDF_MARKDOWN + + +def test_list_publications_parses_api_listing() -> None: + """WHO listing payloads are parsed from the publications OData API.""" + payload = json.loads((_FIXTURES / "who_listing_api.json").read_text(encoding="utf-8")) + + def handler(request: httpx.Request) -> httpx.Response: + assert request.url.path == "/api/hubs/publications" + assert request.url.params["$filter"] == "publishingoffices/any(s:s eq c09761c0-ab8e-4cfa-9744-99509c4d306b)" + assert request.url.params["$skip"] == "0" + return httpx.Response(200, json=payload) + + client = httpx.Client(transport=httpx.MockTransport(handler), base_url=BASE_URL) + + listing_page = list_publications(client) + + assert listing_page == WhoListingPage( + total=356, + refs=[ + WhoPublicationRef( + publication_id="9789240121805", + title=_CVC_GUIDELINE_TITLE, + page_url="https://www.who.int/publications/i/item/9789240121805", + publication_date="28 May 2026", + tag="Guideline", + download_url=_DOWNLOAD_URL, + ), + WhoPublicationRef( + publication_id="9789240121744", + title=_CERVICAL_GUIDELINE_TITLE, + page_url="https://www.who.int/publications/i/item/9789240121744", + publication_date="8 May 2026", + tag="Guideline", + download_url="https://iris.who.int/server/api/core/bitstreams/32214b73-0e95-4243-9e83-617948510dcd/content", + ), + ], + ) + + +def test_publication_ref_from_url_normalizes_publication_url() -> None: + """WHO publication URLs are normalized to canonical refs.""" + assert publication_ref_from_url(_PAGE_URL) == WhoPublicationRef( + publication_id="9789240121805", + title="9789240121805", + page_url=_PAGE_URL, + ) + + +def test_build_publication_text_combines_overview_and_pdf() -> None: + """The guideline body from the PDF is appended to the Overview.""" + content, section_count, title, metadata = build_publication_text( + _page_and_pdf_client(), + _publication_ref(), + pdf_converter=_fake_converter, + ) + + assert title.startswith("Guidelines for the prevention of bloodstream infections") + assert "### Overview" in content + assert "central venous catheters (CVCs)" in content + assert "Use aseptic technique." in content + assert "WHO Team" not in content + assert section_count == 3 + assert metadata["content_scope"] == "full" + assert metadata["pdf_backend"] == "docling" + assert metadata["pdf_bytes"] == len(_PDF_BYTES) + assert metadata["download_url"] == _DOWNLOAD_URL + assert metadata["publication_date"] == "28 May 2026" + assert metadata["tag"] == "Guideline" + assert metadata["isbn"] == "978-92-4-012180-5" + assert metadata["license"] == WHO_LICENSE + assert metadata["listing_category"] == "who-guidelines" + + +def test_build_publication_text_reads_download_url_from_page() -> None: + """A ref without a download URL falls back to the landing-page link.""" + content, _, _, metadata = build_publication_text( + _page_and_pdf_client(), + _publication_ref(download_url=None), + pdf_converter=_fake_converter, + ) + + assert metadata["download_url"] == _DOWNLOAD_URL + assert metadata["content_scope"] == "full" + assert "Use aseptic technique." in content + + +def test_build_publication_text_skips_pdf_when_full_text_disabled() -> None: + """Overview-only scraping leaves the PDF untouched.""" + content, section_count, _, metadata = build_publication_text( + _page_and_pdf_client(), + _publication_ref(), + include_full_text=False, + ) + + assert "### Overview" in content + assert "Use aseptic technique." not in content + assert section_count == 1 + assert metadata["content_scope"] == "overview" + assert metadata["pdf_backend"] is None + assert metadata["pdf_bytes"] is None + + +@pytest.mark.parametrize( + ("pdf_status", "converter"), + [ + pytest.param(200, None, id="conversion-fails"), + pytest.param(404, _fake_converter, id="download-fails"), + ], +) +def test_build_publication_text_falls_back_to_overview(pdf_status: int, converter: object) -> None: + """A broken PDF degrades to the Overview instead of failing the document.""" + + def failing_converter(data: bytes, title: str, publication_id: str) -> str: + raise PdfConversionError("backend exploded") + + content, section_count, _, metadata = build_publication_text( + _page_and_pdf_client(pdf_status=pdf_status), + _publication_ref(), + pdf_converter=converter or failing_converter, + ) + + assert "### Overview" in content + assert "Use aseptic technique." not in content + assert section_count == 1 + assert metadata["content_scope"] == "overview" + assert metadata["pdf_backend"] is None + + +def test_scrape_publication_builds_scraped_document() -> None: + """A WHO publication ref is normalized into a ScrapedDocument.""" + document = scrape_publication( + _page_and_pdf_client(), + _publication_ref(), + link_mode=LinkMode.STRIP, + pdf_converter=_fake_converter, + ) + + assert document.source == "who" + assert document.external_id == "who-9789240121805" + assert document.url == _PAGE_URL + assert document.section_count == 3 + assert document.content.strip() + assert document.metadata["publication_id"] == "9789240121805" + assert document.metadata["content_scope"] == "full" + + +def test_build_publication_text_raises_when_overview_missing() -> None: + """Missing publication markup raises WhoFetchError.""" + html = "

No publication section here.

" + + def handler(request: httpx.Request) -> httpx.Response: + return httpx.Response(200, text=html) + + client = httpx.Client(transport=httpx.MockTransport(handler)) + ref = WhoPublicationRef( + publication_id="9789240121805", + title="Example guideline", + page_url=_PAGE_URL, + ) + + with pytest.raises(WhoFetchError, match="No publication content section"): + build_publication_text(client, ref) diff --git a/pyproject.toml b/pyproject.toml index ba89b1ed..f0dee4d7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,6 +16,7 @@ dev = [ "pytest>=8.0", "ruff>=0.11", ] +pdf = ["amfv-datasets[pdf]"] [tool.uv] package = false diff --git a/uv.lock b/uv.lock index 0bfc4aa8..0e7b0336 100644 --- a/uv.lock +++ b/uv.lock @@ -4,10 +4,12 @@ requires-python = ">=3.13" resolution-markers = [ "python_full_version >= '3.14' and sys_platform == 'win32'", "python_full_version >= '3.14' and sys_platform == 'emscripten'", - "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version >= '3.14' and sys_platform == 'darwin'", + "python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'emscripten' and sys_platform != 'win32'", "python_full_version < '3.14' and sys_platform == 'win32'", "python_full_version < '3.14' and sys_platform == 'emscripten'", - "python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version < '3.14' and sys_platform == 'darwin'", + "python_full_version < '3.14' and sys_platform != 'darwin' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] [manifest] @@ -20,6 +22,24 @@ members = [ "amfv-verifier", ] +[[package]] +name = "accelerate" +version = "1.14.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "huggingface-hub" }, + { name = "numpy" }, + { name = "packaging" }, + { name = "psutil" }, + { name = "pyyaml" }, + { name = "safetensors" }, + { name = "torch" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/8d/75/94cd5d389649578aca399e5aa822637eec18319a1dadc400ffe2f9a7493f/accelerate-1.14.0.tar.gz", hash = "sha256:41b9c4377a54e0b460a959b0defa1b736e4ca0a2373252d9a539964c2afe3c8d", size = 412167, upload-time = "2026-06-11T13:45:52.326Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/a8/db/253133d7e7cb40d3af384bb2f5c0b4a2b7fdcffbc95c688cc67a20a3c103/accelerate-1.14.0-py3-none-any.whl", hash = "sha256:e94390c2863b873be18f623f9df48a0d8fe5eff13ea7f1a00092b0a7904888c6", size = 389246, upload-time = "2026-06-11T13:45:50.477Z" }, +] + [[package]] name = "aiohappyeyeballs" version = "2.6.2" @@ -137,6 +157,9 @@ dev = [ { name = "pytest" }, { name = "ruff" }, ] +pdf = [ + { name = "amfv-datasets", extra = ["pdf"] }, +] [package.metadata] @@ -150,6 +173,7 @@ dev = [ { name = "pytest", specifier = ">=8.0" }, { name = "ruff", specifier = ">=0.11" }, ] +pdf = [{ name = "amfv-datasets", extras = ["pdf"], editable = "datasets" }] [[package]] name = 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