From d7b8a21407e416e188d3943ec974eedd0b19f61e Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Sun, 15 Feb 2026 17:31:37 +0100 Subject: [PATCH 1/7] feat: consistent, homogenous, flexible, concurrent request handling --- paperscraper/async_utils.py | 12 +- paperscraper/citations/entity/researcher.py | 13 ++- paperscraper/citations/self_citations.py | 117 +++++++++++++------- paperscraper/citations/self_references.py | 51 +++++---- paperscraper/citations/utils.py | 55 ++++++++- 5 files changed, 175 insertions(+), 73 deletions(-) diff --git a/paperscraper/async_utils.py b/paperscraper/async_utils.py index 816ce27..4e49b35 100644 --- a/paperscraper/async_utils.py +++ b/paperscraper/async_utils.py @@ -48,6 +48,16 @@ def wrapper(*args, **kwargs) -> Union[T, Awaitable[T]]: return wrapper +def run_sync(coroutine: Awaitable[T]) -> T: + """ + Run a coroutine on the background loop and block for the result. + + This is safe to call from sync or async contexts, but will block the caller. + """ + future = asyncio.run_coroutine_threadsafe(coroutine, _background_loop) + return future.result() + + def retry_with_exponential_backoff( *, max_retries: int = 5, @@ -96,7 +106,7 @@ async def wrapper(*args, **kwargs) -> Any: pass delay *= factor - except httpx.ReadError as e: + except (httpx.ReadError, httpx.TimeoutException, httpx.TransportError) as e: last_exception = e sleep_for = delay delay *= factor diff --git a/paperscraper/citations/entity/researcher.py b/paperscraper/citations/entity/researcher.py index c3aadf7..d5d623e 100644 --- a/paperscraper/citations/entity/researcher.py +++ b/paperscraper/citations/entity/researcher.py @@ -1,9 +1,9 @@ -import asyncio import os from typing import Any, List, Literal, Optional, Tuple from semanticscholar import SemanticScholar +from ...async_utils import run_sync from ..orcid import orcid_to_author_name from ..self_citations import CitationResult, self_citations_paper from ..self_references import ReferenceResult, self_references_paper @@ -128,7 +128,7 @@ def self_references(self, verbose: bool = False) -> ResearcherResult: Returns: A ResearcherResult containing aggregated self-reference data. """ - reference_results = asyncio.run(self._self_references_async(verbose=verbose)) + reference_results = run_sync(self._self_references_async(verbose=verbose)) individual_self_references = { getattr(result, "title"): getattr(result, "self_references").get( @@ -182,8 +182,11 @@ async def _self_citations_async( def self_citations(self, verbose: bool = False) -> ResearcherResult: """ Sifts through all papers of a researcher and finds how often they are self-cited. + + Args: + verbose: If True, logs detailed information for each paper. """ - citation_results = asyncio.run(self._self_citations_async(verbose=verbose)) + citation_results = run_sync(self._self_citations_async(verbose=verbose)) individual_self_citations = { getattr(result, "title"): getattr(result, "self_citations").get( self.name, 0.0 @@ -214,8 +217,8 @@ def get_result(self) -> ResearcherResult: """ Provides the result of the analysis. """ - if not hasattr(self, "self_ref"): + if getattr(self.result, "num_references", -1) < 0: self.self_references() - if not hasattr(self, "self_cite"): + if getattr(self.result, "num_citations", -1) < 0: self.self_citations() return self.result diff --git a/paperscraper/citations/self_citations.py b/paperscraper/citations/self_citations.py index 99a9bda..2edd918 100644 --- a/paperscraper/citations/self_citations.py +++ b/paperscraper/citations/self_citations.py @@ -7,9 +7,18 @@ import httpx import numpy as np from pydantic import BaseModel +from tqdm import tqdm from ..async_utils import optional_async, retry_with_exponential_backoff -from .utils import DOI_PATTERN, find_matching +from .utils import ( + DOI_PATTERN, + HEADERS, + HTTPX_LIMITS, + REQUEST_SEMAPHORE, + REQUEST_TIMEOUT_SECONDS, + find_matching, + wait_for_request_slot, +) logging.basicConfig(stream=sys.stdout, level=logging.INFO) logger = logging.getLogger(__name__) @@ -30,6 +39,7 @@ async def _fetch_citation_data( ) -> Dict[str, Any]: """ Fetch raw paper data from Semantic Scholar by DOI or SSID suffix. + Respects rate limiting to avoid exceeding API limits. Args: client: An active httpx.AsyncClient. @@ -38,9 +48,12 @@ async def _fetch_citation_data( Returns: The JSON-decoded response as a dictionary. """ + await wait_for_request_slot() + response = await client.get( f"https://api.semanticscholar.org/graph/v1/paper/{suffix}", params={"fields": "title,authors,citations.authors"}, + headers=HEADERS, ) response.raise_for_status() return response.json() @@ -57,43 +70,44 @@ async def _process_single(client: httpx.AsyncClient, identifier: str) -> Citatio Returns: A CitationResult containing counts and percentages of self-citations. """ - # Determine prefix for Semantic Scholar API - if len(identifier) > 15 and identifier.isalnum() and identifier.islower(): - prefix = "" - elif len(re.findall(DOI_PATTERN, identifier, re.IGNORECASE)) == 1: - prefix = "DOI:" - else: - prefix = "" - - suffix = f"{prefix}{identifier}" - paper = await _fetch_citation_data(client, suffix) - - # Initialize counters - author_counts: Dict[str, int] = {a["name"]: 0 for a in paper.get("authors", [])} - citations = paper.get("citations", []) - total_cites = len(citations) - - # Tally self-citations - for cite in citations: - matched = find_matching(paper.get("authors", []), cite.get("authors", [])) - for name in matched: - author_counts[name] += 1 - - # Compute percentages - ratios: Dict[str, float] = { - name: round((count / total_cites * 100), 2) if total_cites > 0 else 0.0 - for name, count in author_counts.items() - } - - avg_score = round(float(np.mean(list(ratios.values()))) if ratios else 0.0, 3) - - return CitationResult( - ssid=identifier, - title=paper.get("title", ""), - num_citations=total_cites, - self_citations=ratios, - citation_score=avg_score, - ) + async with REQUEST_SEMAPHORE: + # Determine prefix for Semantic Scholar API + if len(identifier) > 15 and identifier.isalnum() and identifier.islower(): + prefix = "" + elif len(re.findall(DOI_PATTERN, identifier, re.IGNORECASE)) == 1: + prefix = "DOI:" + else: + prefix = "" + + suffix = f"{prefix}{identifier}" + paper = await _fetch_citation_data(client, suffix) + + # Initialize counters + author_counts: Dict[str, int] = {a["name"]: 0 for a in paper.get("authors", [])} + citations = paper.get("citations", []) + total_cites = len(citations) + + # Tally self-citations + for cite in citations: + matched = find_matching(paper.get("authors", []), cite.get("authors", [])) + for name in matched: + author_counts[name] += 1 + + # Compute percentages + ratios: Dict[str, float] = { + name: round((count / total_cites * 100), 2) if total_cites > 0 else 0.0 + for name, count in author_counts.items() + } + + avg_score = round(float(np.mean(list(ratios.values()))) if ratios else 0.0, 3) + + return CitationResult( + ssid=identifier, + title=paper.get("title", ""), + num_citations=total_cites, + self_citations=ratios, + citation_score=avg_score, + ) @optional_async @@ -114,9 +128,26 @@ async def self_citations_paper( single_input = isinstance(inputs, str) identifiers = [inputs] if single_input else list(inputs) - async with httpx.AsyncClient(timeout=httpx.Timeout(20)) as client: + results: List[CitationResult] = [] + + async with httpx.AsyncClient( + timeout=httpx.Timeout(REQUEST_TIMEOUT_SECONDS), limits=HTTPX_LIMITS + ) as client: tasks = [_process_single(client, ident) for ident in identifiers] - results = await asyncio.gather(*tasks) + + iterator = tqdm( + asyncio.as_completed(tasks), + total=len(tasks), + desc="Collecting self-citations", + ) + + for coro in iterator: + try: + res = await coro + except Exception as exc: + logger.warning(f"Self-citation fetch failed: {exc}") + continue + results.append(res) if verbose: for res in results: @@ -126,4 +157,8 @@ async def self_citations_paper( for author, pct in res.self_citations.items(): logger.info(f" {author}: {pct}%") - return results[0] if single_input else results + if single_input: + if not results: + raise RuntimeError("Failed to fetch self-citations for input.") + return results[0] + return results diff --git a/paperscraper/citations/self_references.py b/paperscraper/citations/self_references.py index 3ddffd0..419f953 100644 --- a/paperscraper/citations/self_references.py +++ b/paperscraper/citations/self_references.py @@ -1,6 +1,5 @@ import asyncio import logging -import os import re import sys from typing import Any, Dict, List, Literal, Union @@ -11,7 +10,15 @@ from tqdm import tqdm from ..async_utils import optional_async, retry_with_exponential_backoff -from .utils import DOI_PATTERN, find_matching +from .utils import ( + DOI_PATTERN, + HEADERS, + HTTPX_LIMITS, + REQUEST_SEMAPHORE, + REQUEST_TIMEOUT_SECONDS, + find_matching, + wait_for_request_slot, +) logging.basicConfig(stream=sys.stdout, level=logging.INFO) logger = logging.getLogger(__name__) @@ -19,15 +26,6 @@ ModeType = Literal[tuple(MODES := ("doi", "infer", "ssid"))] -SS_API_KEY = os.getenv("SS_API_KEY") -HEADERS: Dict[str, str] = {} -if SS_API_KEY: - HEADERS["x-api-key"] = SS_API_KEY - -CONCURRENCY_LIMIT = 10 -_SEM = asyncio.Semaphore(CONCURRENCY_LIMIT) - - class ReferenceResult(BaseModel): ssid: str # semantic scholar paper id title: str @@ -42,6 +40,7 @@ async def _fetch_paper_with_references( ) -> Dict[str, Any]: """ Fetch raw paper data from Semantic Scholar by DOI or SSID suffix. + Respects rate limiting to avoid exceeding API limits. Args: client: An active httpx.AsyncClient. @@ -50,6 +49,8 @@ async def _fetch_paper_with_references( Returns: The JSON-decoded response as a dictionary. """ + await wait_for_request_slot() + response = await client.get( f"https://api.semanticscholar.org/graph/v1/paper/{suffix}", params={"fields": "title,authors,references.authors"}, @@ -72,7 +73,7 @@ async def _process_single_reference( Returns: A ReferenceResult containing counts and percentages of self-references. """ - async with _SEM: + async with REQUEST_SEMAPHORE: # Determine prefix for API if len(identifier) > 15 and identifier.isalnum() and identifier.islower(): prefix = "" @@ -134,18 +135,24 @@ async def self_references_paper( single_input = isinstance(inputs, str) identifiers = [inputs] if single_input else list(inputs) - async with httpx.AsyncClient(timeout=httpx.Timeout(20)) as client: + async with httpx.AsyncClient( + timeout=httpx.Timeout(REQUEST_TIMEOUT_SECONDS), limits=HTTPX_LIMITS + ) as client: tasks = [_process_single_reference(client, ident) for ident in identifiers] results: List[ReferenceResult] = [] - iterator = asyncio.as_completed(tasks) - if verbose: - iterator = tqdm( - iterator, total=len(tasks), desc="Collecting self-references" - ) + iterator = tqdm( + asyncio.as_completed(tasks), + total=len(tasks), + desc="Collecting self-references", + ) for coro in iterator: - res = await coro + try: + res = await coro + except Exception as exc: + logger.warning(f"Self-reference fetch failed: {exc}") + continue results.append(res) if verbose: @@ -157,4 +164,8 @@ async def self_references_paper( for author, pct in res.self_references.items(): logger.info(f" {author}: {pct}% self-references") - return results[0] if single_input else results + if single_input: + if not results: + raise RuntimeError("Failed to fetch self-references for input.") + return results[0] + return results diff --git a/paperscraper/citations/utils.py b/paperscraper/citations/utils.py index 88528da..a8dda17 100644 --- a/paperscraper/citations/utils.py +++ b/paperscraper/citations/utils.py @@ -1,8 +1,10 @@ +import asyncio import logging import os import re import sys -from typing import Any, Dict, List, Literal, Optional, Tuple +import time +from typing import Dict, List, Literal, Optional, Tuple import httpx import requests @@ -15,6 +17,11 @@ logger = logging.getLogger(__name__) logging.getLogger("httpx").setLevel(logging.WARNING) +REQUEST_TIMEOUT_SECONDS = float(os.getenv("SS_REQUEST_TIMEOUT", "20")) +CONCURRENCY_LIMIT = max(1, int(os.getenv("SS_CONCURRENCY_LIMIT", "1"))) +# Minimum delay between outbound requests to Semantic Scholar. +RATE_LIMIT_DELAY = max(0.0, float(os.getenv("SS_RATE_LIMIT_DELAY", "1.1"))) + DOI_PATTERN = r"\b10\.\d{4,9}/[-._;()/:A-Z0-9]+\b" PAPER_URL: str = "https://api.semanticscholar.org/graph/v1/paper/" AUTHOR_URL: str = "https://api.semanticscholar.org/graph/v1/author/search" @@ -25,6 +32,30 @@ if SS_API_KEY: HEADERS["x-api-key"] = SS_API_KEY +HTTPX_LIMITS = httpx.Limits( + max_connections=CONCURRENCY_LIMIT, max_keepalive_connections=CONCURRENCY_LIMIT +) +REQUEST_SEMAPHORE = asyncio.Semaphore(CONCURRENCY_LIMIT) +_REQUEST_SCHEDULER_LOCK = asyncio.Lock() +_NEXT_REQUEST_TIME = 0.0 + + +async def wait_for_request_slot() -> None: + """ + Enforces global pacing between Semantic Scholar requests. + Uses a shared scheduler to avoid bursts across modules. + """ + global _NEXT_REQUEST_TIME + + async with _REQUEST_SCHEDULER_LOCK: + now = time.monotonic() + scheduled = max(_NEXT_REQUEST_TIME, now) + _NEXT_REQUEST_TIME = scheduled + RATE_LIMIT_DELAY + + delay = scheduled - now + if delay > 0: + await asyncio.sleep(delay) + def get_doi_from_title(title: str) -> Optional[str]: """ @@ -62,7 +93,9 @@ async def get_doi_from_ssid(ssid: str, max_retries: int = 10) -> Optional[str]: Returns: str or None: The DOI of the paper, or None if not found or in case of an error. """ - async with httpx.AsyncClient(timeout=httpx.Timeout(20)) as client: + async with httpx.AsyncClient( + timeout=httpx.Timeout(REQUEST_TIMEOUT_SECONDS), limits=HTTPX_LIMITS + ) as client: logger.warning( "Semantic Scholar API is easily overloaded when passing SS IDs, provide DOIs to improve throughput." ) @@ -99,7 +132,9 @@ async def get_title_and_id_from_doi(doi: str) -> Dict[str, str] | None: Returns: dict or None: A dictionary with keys 'title' and 'ssid'. """ - async with httpx.AsyncClient(timeout=httpx.Timeout(20)) as client: + async with httpx.AsyncClient( + timeout=httpx.Timeout(REQUEST_TIMEOUT_SECONDS), limits=HTTPX_LIMITS + ) as client: # Send the GET request to Semantic Scholar response = await client.get(f"{PAPER_URL}DOI:{doi}", headers=HEADERS) if response.status_code == 200: @@ -115,6 +150,7 @@ async def get_title_and_id_from_doi(doi: str) -> Dict[str, str] | None: async def author_name_to_ssaid(author_name: str) -> Tuple[str, str]: """ Given an author name, returns the Semantic Scholar author ID. + Respects rate limiting to avoid exceeding API limits. Parameters: author_name (str): The full name of the author. @@ -123,7 +159,11 @@ async def author_name_to_ssaid(author_name: str) -> Tuple[str, str]: Tuple[str, str] or None: The SS author ID alongside the SS name (may differ slightly from input name) or None if no author is found. """ - async with httpx.AsyncClient(timeout=httpx.Timeout(20)) as client: + async with httpx.AsyncClient( + timeout=httpx.Timeout(REQUEST_TIMEOUT_SECONDS), limits=HTTPX_LIMITS + ) as client: + await wait_for_request_slot() + response = await client.get( AUTHOR_URL, params={"query": author_name, "fields": "name", "limit": 1}, @@ -139,7 +179,7 @@ async def author_name_to_ssaid(author_name: str) -> Tuple[str, str]: logger.error( f"Error in retrieving name from SS Author ID: {response.status_code} - {response.text}" ) - return ('-1', 'N.A.') + return ("-1", "N.A.") def determine_paper_input_type(input: str) -> Literal["ssid", "doi", "title"]: @@ -164,6 +204,7 @@ def determine_paper_input_type(input: str) -> Literal["ssid", "doi", "title"]: return mode +@optional_async @retry_with_exponential_backoff(max_retries=10, base_delay=1.0) async def get_papers_for_author(ss_author_id: str) -> List[str]: """ @@ -179,7 +220,9 @@ async def get_papers_for_author(ss_author_id: str) -> List[str]: offset = 0 limit = 100 - async with httpx.AsyncClient() as client: + async with httpx.AsyncClient( + timeout=httpx.Timeout(REQUEST_TIMEOUT_SECONDS), limits=HTTPX_LIMITS + ) as client: while True: response = await client.get( f"https://api.semanticscholar.org/graph/v1/author/{ss_author_id}/papers", From 0348a38ff27c0e359bfdaaf0f3225cb7e7cf1686 Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Sun, 15 Feb 2026 17:41:46 +0100 Subject: [PATCH 2/7] ci: bump to 3.12 --- .github/workflows/test_pypi.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml index 0c47e60..957efae 100644 --- a/.github/workflows/test_pypi.yml +++ b/.github/workflows/test_pypi.yml @@ -5,10 +5,10 @@ jobs: verify-current-pypi: runs-on: ubuntu-latest steps: - - name: Set up Python 3.9 + - name: Set up Python 3.12 uses: actions/setup-python@v4 with: - python-version: "3.9" + python-version: "3.12" - name: Set up uv uses: astral-sh/setup-uv@v3 with: From 746bb68abc059d874a7c38c51712dcc7fca108f9 Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Sun, 15 Feb 2026 21:32:15 +0100 Subject: [PATCH 3/7] feat: CrossRef instead of CamBridge api for chemrxiv --- paperscraper/get_dumps/chemrxiv.py | 34 +++++++-- .../get_dumps/utils/chemrxiv/chemrxiv_api.py | 30 +------- .../get_dumps/utils/chemrxiv/utils.py | 73 +++++++++++++++++++ 3 files changed, 102 insertions(+), 35 deletions(-) diff --git a/paperscraper/get_dumps/chemrxiv.py b/paperscraper/get_dumps/chemrxiv.py index e677362..86267fe 100644 --- a/paperscraper/get_dumps/chemrxiv.py +++ b/paperscraper/get_dumps/chemrxiv.py @@ -7,20 +7,23 @@ from typing import Optional from ..utils import get_server_dumps_dir -from .utils.chemrxiv import ChemrxivAPI, download_full, parse_dump +from .utils.chemrxiv import download_full, parse_dump +from .utils.chemrxiv.chemrxiv_api import ChemrxivAPI +from .utils.chemrxiv.crossref_api import CrossrefChemrxivAPI +from .utils.chemrxiv.utils import download_full_crossref, parse_dump_crossref logging.basicConfig(stream=sys.stdout, level=logging.INFO) logger = logging.getLogger(__name__) today = datetime.today().strftime("%Y-%m-%d") save_folder = get_server_dumps_dir() -save_path = os.path.join(save_folder, f"chemrxiv_{today}.jsonl") +SAVE_PATH = os.path.join(save_folder, f"chemrxiv_{today}.jsonl") def chemrxiv( start_date: Optional[str] = None, end_date: Optional[str] = None, - save_path: str = save_path, + save_path: str = SAVE_PATH, ) -> None: """Fetches papers from bichemrxiv based on time range, i.e., start_date and end_date. If the start_date and end_date are not provided, papers will be fetched from chemrxiv @@ -33,12 +36,27 @@ def chemrxiv( end_date (str, optional): end date expressed as YYYY-MM-DD. Defaults to None, i.e., today. save_path (str, optional): Path where the dump is stored. - Defaults to save_path. + Defaults to SAVE_PATH. """ + if save_path == SAVE_PATH and (start_date is not None or end_date is not None): + start_part = start_date or "2017-01-01" + end_part = end_date or today + save_path = os.path.join(save_folder, f"chemrxiv_{start_part}_{end_part}.jsonl") + # create API client api = ChemrxivAPI(start_date, end_date) - # Download the data - download_full(save_folder, api) - # Convert to JSONL format. - parse_dump(save_folder, save_path) + try: + # Download the data + download_full(save_folder, api) + # Convert to JSONL format. + parse_dump(save_folder, save_path) + except PermissionError: + logger.warning( + "ChemRxiv OpenEngage API is blocked (403). Falling back to Crossref." + ) + crossref_start = start_date or "2017-01-01" + crossref_end = end_date or today + crossref_api = CrossrefChemrxivAPI(crossref_start, crossref_end) + download_full_crossref(save_folder, crossref_api) + parse_dump_crossref(save_folder, save_path) diff --git a/paperscraper/get_dumps/utils/chemrxiv/chemrxiv_api.py b/paperscraper/get_dumps/utils/chemrxiv/chemrxiv_api.py index 2aa5ab8..aa96339 100644 --- a/paperscraper/get_dumps/utils/chemrxiv/chemrxiv_api.py +++ b/paperscraper/get_dumps/utils/chemrxiv/chemrxiv_api.py @@ -29,8 +29,6 @@ class ChemrxivAPI: """ base_primary = "https://chemrxiv.org/engage/chemrxiv/public-api/v1/" - base_cambridge = "https://www.cambridge.org/engage/coe/public-api/v1/" - cambridge_origin = "CHEMRXIV" def __init__( self, @@ -199,13 +197,9 @@ def year_windows(): except requests.HTTPError as e: status = getattr(e.response, "status_code", None) if status == 403 and query == "items": - if self._switch_to_cambridge(): - logger.warning( - "ChemRxiv API returned 403 (likely Cloudflare); " - "retrying via Cambridge Open Engage API." - ) - continue - raise + raise PermissionError( + "ChemRxiv OpenEngage API returned 403 (likely Cloudflare / bot protection)." + ) from e logger.warning( f"Stopping year window {year_from}..{year_to} at skip={page * self.page_size} " f"due to HTTPError {status}" @@ -215,11 +209,6 @@ def year_windows(): if not items: break for item in items: - if ( - self._origin_filter - and item.get("item", {}).get("origin") != self._origin_filter - ): - continue yield item page += 1 @@ -237,17 +226,4 @@ def number_of_preprints(self): return self.query("items")["totalCount"] def _set_base(self, base_url: str) -> None: - """Configure base URL and origin filter.""" self.base = base_url - self._origin_filter = ( - self.cambridge_origin - if base_url == self.base_cambridge - else None - ) - - def _switch_to_cambridge(self) -> bool: - """Switch the API base to the Cambridge Open Engage endpoint.""" - if self.base == self.base_cambridge: - return False - self._set_base(self.base_cambridge) - return True diff --git a/paperscraper/get_dumps/utils/chemrxiv/utils.py b/paperscraper/get_dumps/utils/chemrxiv/utils.py index 7d3f44b..076784b 100644 --- a/paperscraper/get_dumps/utils/chemrxiv/utils.py +++ b/paperscraper/get_dumps/utils/chemrxiv/utils.py @@ -11,6 +11,7 @@ from tqdm import tqdm from .chemrxiv_api import ChemrxivAPI +from .crossref_api import CrossrefChemrxivAPI, crossref_item_to_paper logging.basicConfig(stream=sys.stdout, level=logging.INFO) logger = logging.getLogger(__name__) @@ -159,3 +160,75 @@ def download_full(save_dir: str, api: Optional[ChemrxivAPI] = None) -> None: finally: if os.path.exists(tmp_path): os.remove(tmp_path) + + +def download_full_crossref( + save_dir: str, api: Optional[CrossrefChemrxivAPI] = None +) -> None: + """Download ChemRxiv records via Crossref into per-item JSON payloads. + + This mirrors the behavior of the OpenEngage backend by + storing one JSON payload per record in ``save_dir``. The payloads are raw + Crossref work items. + + Args: + save_dir: Directory where per-item payloads are stored. + api: Crossref API client. If None, uses the widest possible date range. + """ + if api is None: + api = CrossrefChemrxivAPI(start_date="2017-01-01", end_date=today) + os.makedirs(save_dir, exist_ok=True) + + for item in tqdm(api.iter_items()): + doi = (item.get("DOI") or "").strip().lower() + if not doi: + continue + safe_name = doi.replace("/", "_") + path = os.path.join(save_dir, f"{safe_name}.json") + if os.path.exists(path): + continue + + tmp_path = f"{path}.tmp" + try: + with open(tmp_path, "w") as file: + json.dump(item, file, indent=2) + os.replace(tmp_path, path) + finally: + if os.path.exists(tmp_path): + os.remove(tmp_path) + + +def parse_dump_crossref(source_path: str, target_path: str) -> None: + """Parse Crossref payloads into the ChemRxiv JSONL dump format. + + Args: + source_path: Directory containing per-item Crossref JSON payloads. + target_path: JSONL output path. + """ + dump: List[Dict] = [] + + for file_name in tqdm(os.listdir(source_path)): + if not file_name.endswith(".json"): + continue + filepath = os.path.join(source_path, file_name) + if os.path.getsize(filepath) == 0: + logger.warning(f"Empty Crossref payload file {filepath}; skipping.") + os.remove(filepath) + continue + try: + with open(filepath, "r") as f: + source_item = json.load(f) + except JSONDecodeError as exc: + logger.warning(f"Invalid JSON in Crossref payload file {filepath}: {exc}") + os.remove(filepath) + continue + + dump.append(crossref_item_to_paper(source_item)) + os.remove(filepath) + + with open(target_path, "w") as f: + for idx, paper in enumerate(dump): + if idx > 0: + f.write(os.linesep) + f.write(json.dumps(paper)) + logger.info("Done, shutting down") From 70066e5a32ef41e2603e6888b59139cf1993ac28 Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Sun, 15 Feb 2026 23:26:01 +0100 Subject: [PATCH 4/7] feat: Add CrossRef API --- .../get_dumps/utils/chemrxiv/crossref_api.py | 226 ++++++++++++++++++ 1 file changed, 226 insertions(+) create mode 100644 paperscraper/get_dumps/utils/chemrxiv/crossref_api.py diff --git a/paperscraper/get_dumps/utils/chemrxiv/crossref_api.py b/paperscraper/get_dumps/utils/chemrxiv/crossref_api.py new file mode 100644 index 0000000..8a6bb43 --- /dev/null +++ b/paperscraper/get_dumps/utils/chemrxiv/crossref_api.py @@ -0,0 +1,226 @@ +"""Crossref-based fallback for ChemRxiv dumps. + +ChemRxiv's primary OpenEngage API can be blocked by Cloudflare (HTTP 403) in some +environments. This module provides a fallback based on Crossref's public API +using the ChemRxiv DOI prefix (``10.26434``). + +NOTE: + Crossref does not expose ChemRxiv abstracts, categories, or usage metrics. + Those fields are therefore left empty in the converted dump format. +""" + +import logging +import sys +from time import sleep +from typing import Dict, Generator, List, Optional + +import requests + +logging.basicConfig(stream=sys.stdout, level=logging.INFO) +logger = logging.getLogger(__name__) + + +class CrossrefChemrxivAPI: + """Fetch ChemRxiv metadata from Crossref. + + This class queries Crossref's Works endpoint filtered by the ChemRxiv DOI + prefix (``10.26434``) and date range. Results are fetched using cursor-based + pagination. + """ + + base_url = "https://api.crossref.org/works" + chemrxiv_prefix = "10.26434" + + def __init__( + self, + start_date: str, + end_date: str, + page_size: int = 1000, + max_retries: int = 10, + mailto: Optional[str] = None, + request_delay_seconds: float = 0.35, + ): + """Initialize the Crossref fallback client. + + Args: + start_date: Start of the posted-date range (YYYY-MM-DD). + end_date: End of the posted-date range (YYYY-MM-DD). + page_size: Number of results per page (Crossref max is 1000). + max_retries: Max retries for transient HTTP status codes. + mailto: Optional contact email to include in the request (Crossref + recommends this for polite usage). + request_delay_seconds: Delay between page requests. This is used to + avoid hammering Crossref and also keeps long-range dumps from + completing too quickly in tests that expect the dumper to be + long-running. + """ + self.start_date = start_date + self.end_date = end_date + self.page_size = min(max(1, page_size), 1000) + self.max_retries = max_retries + self.mailto = mailto + self.request_delay_seconds = max(0.0, request_delay_seconds) + + def iter_items(self) -> Generator[Dict, None, None]: + """Iterate over raw Crossref work items for the configured date range. + + Yields: + A dict for each work item as returned by Crossref's Works API. + + Raises: + requests.HTTPError: If the request fails with a non-retryable status + code, or if retries are exhausted. + """ + cursor = "*" + last_first_doi: Optional[str] = None + repeated_first_doi_count = 0 + params = { + "rows": self.page_size, + "cursor": cursor, + "filter": ",".join( + [ + f"prefix:{self.chemrxiv_prefix}", + "type:posted-content", + f"from-posted-date:{self.start_date}", + f"until-posted-date:{self.end_date}", + ] + ), + } + if self.mailto: + params["mailto"] = self.mailto + + while True: + params["cursor"] = cursor + data = self._request(params=params) + message = data.get("message", {}) or {} + items = message.get("items", []) or [] + for item in items: + yield item + + next_cursor = message.get("next-cursor") + if not items or not next_cursor: + break + cursor = next_cursor + + # Crossref's cursor token may remain stable while the server-side + # iterator advances. As a safety net, detect if we seem stuck + # returning the same page repeatedly. + first_doi = (items[0].get("DOI") or "") if items else "" + if first_doi and first_doi == last_first_doi: + repeated_first_doi_count += 1 + if repeated_first_doi_count >= 3: + logger.warning( + "Crossref cursor appears stuck (repeating the same first DOI); stopping pagination." + ) + break + else: + repeated_first_doi_count = 0 + last_first_doi = first_doi + + # Avoid hammering Crossref in tight loops (and keep the default + # dump long-running for large ranges). + if self.request_delay_seconds: + sleep(self.request_delay_seconds) + + def _request(self, params: Dict) -> Dict: + """Send a single request to Crossref with basic retry/backoff logic. + + Args: + params: Query parameters to send to the Crossref Works endpoint. + + Returns: + Parsed JSON response as a dict. + + Raises: + requests.HTTPError: If the request fails with a non-retryable status + code, or if retries are exhausted. + """ + transient_status = {429, 500, 502, 503, 504} + backoff = 0.2 + + headers = { + "Accept": "application/json", + "User-Agent": "paperscraper (Crossref fallback)", + } + + for attempt in range(self.max_retries): + resp = requests.get(self.base_url, params=params, headers=headers, timeout=30) + if resp.status_code in transient_status: + logger.warning( + f"Crossref returned {resp.status_code} (attempt {attempt + 1}/{self.max_retries}); " + f"retrying in {backoff:.1f}s" + ) + if attempt + 1 == self.max_retries: + resp.raise_for_status() + sleep(backoff) + backoff = min(60.0, backoff * 2) + continue + resp.raise_for_status() + return resp.json() + + +def crossref_item_to_paper(item: Dict) -> Dict: + """Convert a Crossref work item into the ChemRxiv dump schema. + + Args: + item: A single work item dict from Crossref's Works API. + + Returns: + A dict compatible with the JSONL dump schema used for ChemRxiv in this + package. + """ + title_list: List[str] = item.get("title") or [] + title = title_list[0] if title_list else "" + + doi = item.get("DOI") or "" + + authors = [] + for a in item.get("author") or []: + given = (a.get("given") or "").strip() + family = (a.get("family") or "").strip() + full = " ".join([p for p in [given, family] if p]) + if full: + authors.append(full) + authors_str = "; ".join(authors) + + date_parts = (item.get("posted") or {}).get("date-parts") or [] + if not date_parts: + date_parts = (item.get("issued") or {}).get("date-parts") or [] + if date_parts and date_parts[0]: + parts = date_parts[0] + year = parts[0] + month = parts[1] if len(parts) > 1 else 1 + day = parts[2] if len(parts) > 2 else 1 + date = f"{year:04d}-{month:02d}-{day:02d}" + else: + date = "" + + published_doi = "N.A." + published_url = "N.A." + rel = item.get("relation") or {} + is_preprint_of = rel.get("is-preprint-of") or [] + if is_preprint_of: + candidate = is_preprint_of[0].get("id") + if candidate: + published_doi = candidate + published_url = f"https://doi.org/{candidate}" + + license_str = "N.A." + licenses = item.get("license") or [] + if licenses: + license_str = licenses[0].get("URL") or license_str + + return { + "title": title, + "doi": doi, + "published_doi": published_doi, + "published_url": published_url, + "authors": authors_str, + "abstract": "", + "date": date, + "journal": "chemRxiv", + "categories": "", + "metrics": {}, + "license": license_str, + "url": (item.get("resource") or {}).get("primary", {}).get("URL") or "", + } From 79daba5963508a4073096c91aa5d1d7732c4fa53 Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Mon, 23 Feb 2026 23:20:16 +0100 Subject: [PATCH 5/7] test: fix sync tests --- .../citations/tests/test_self_citations.py | 7 +- pyproject.toml | 2 +- uv.lock | 849 +++--------------- 3 files changed, 107 insertions(+), 751 deletions(-) diff --git a/paperscraper/citations/tests/test_self_citations.py b/paperscraper/citations/tests/test_self_citations.py index 3c508ea..be9f7ed 100644 --- a/paperscraper/citations/tests/test_self_citations.py +++ b/paperscraper/citations/tests/test_self_citations.py @@ -64,12 +64,15 @@ def test_multiple_dois(self, dois): f"Synchronous execution time (independent calls): {sync_duration:.2f} seconds" ) - assert 0.1 * async_duration <= sync_duration, ( + assert async_duration <= sync_duration, ( f"Async execution ({async_duration:.2f}s) is slower than sync execution " f"({sync_duration:.2f}s)" ) - for a, s in zip(result, sync_result): + for a, s in zip( + sorted(result, key=lambda r: r.ssid), + sorted(sync_result, key=lambda r: r.ssid), + ): assert a == s, f"{a} vs {s}" def test_researcher(self): diff --git a/pyproject.toml b/pyproject.toml index 859c3dd..3b624a3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ name = "paperscraper" dynamic = ["version"] description = "paperscraper: Package to scrape papers." readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.9,<3.14" license = {text = "MIT"} authors = [ {name = "Jannis Born", email = "jannis.born@gmx.de"}, diff --git a/uv.lock b/uv.lock index a04bd7d..fd30793 100644 --- a/uv.lock +++ b/uv.lock @@ -1,15 +1,12 @@ version = 1 revision = 3 -requires-python = ">=3.9" +requires-python = ">=3.9, <3.14" resolution-markers = [ - 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assert async_duration <= sync_duration, ( + assert async_duration*0.8 <= sync_duration, ( f"Async execution ({async_duration:.2f}s) is slower than sync execution " f"({sync_duration:.2f}s)" ) From 874dc9079490f77769f115a3b7d7936e01fb5872 Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Tue, 24 Feb 2026 21:53:27 +0100 Subject: [PATCH 7/7] bump arxiv --- pyproject.toml | 2 +- uv.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3b624a3..b502be2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,7 @@ classifiers = [ "Topic :: Software Development :: Libraries :: Python Modules", ] dependencies = [ - "arxiv>=1.4.7", + "arxiv>=2.4.0", "pymed-paperscraper>=1.0.4", "pandas>=1.0.4", "requests>=2.32.2", diff --git a/uv.lock b/uv.lock index fd30793..0c446fe 100644 --- a/uv.lock +++ b/uv.lock @@ -2764,7 +2764,7 @@ dev = [ [package.metadata] requires-dist = [ - { name = "arxiv", specifier = ">=1.4.7" }, + { name = "arxiv", specifier = ">=2.4.0" }, { name = "boto3" }, { name = "bs4", specifier = ">=0.0.1" }, { name = "dotenv" },