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224 | class SemanticScholarReader(BaseReader):
"""
A class to read and process data from Semantic Scholar API
...
Methods:
-------
__init__():
Instantiate the SemanticScholar object
load_data(query: str, limit: int = 10, returned_fields: list = ["title", "abstract", "venue", "year", "paperId", "citationCount", "openAccessPdf", "authors"]) -> list:
Loads data from Semantic Scholar based on the query and returned_fields
"""
def __init__(self, timeout=10, api_key=None, base_dir="pdfs") -> None:
"""
Instantiate the SemanticScholar object.
"""
import arxiv
from semanticscholar import SemanticScholar
self.arxiv = arxiv
self.base_dir = base_dir
self.s2 = SemanticScholar(timeout, api_key)
# check for base dir
if not os.path.exists(self.base_dir):
os.makedirs(self.base_dir)
def _clear_cache(self):
"""
delete the .citation* folder.
"""
import shutil
shutil.rmtree("./.citation*")
def _download_pdf(self, paper_id, url: str, base_dir="pdfs"):
logger = logging.getLogger()
headers = {
"User-Agent": (
"Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML,"
" like Gecko) Chrome/58.0.3029.110 Safari/537.3"
)
}
# Making a GET request
response = requests.get(url, headers=headers, stream=True)
content_type = response.headers["Content-Type"]
# As long as the content-type is application/pdf, this will download the file
if "application/pdf" in content_type:
os.makedirs(base_dir, exist_ok=True)
file_path = os.path.join(base_dir, f"{paper_id}.pdf")
# check if the file already exists
if os.path.exists(file_path):
logger.info(f"{file_path} already exists")
return file_path
with open(file_path, "wb") as file:
for chunk in response.iter_content(chunk_size=1024):
if chunk:
file.write(chunk)
logger.info(f"Downloaded pdf from {url}")
return file_path
else:
logger.warning(f"{url} was not downloaded: protected")
return None
def _get_full_text_docs(self, documents: List[Document]) -> List[Document]:
from PyPDF2 import PdfReader
"""
Gets the full text of the documents from Semantic Scholar
Parameters
----------
documents: list
The list of Document object that contains the search results
Returns
-------
list
The list of Document object that contains the search results with full text
Raises
------
Exception
If there is an error while getting the full text
"""
full_text_docs = []
for paper in documents:
metadata = paper.extra_info
url = metadata["openAccessPdf"]
externalIds = metadata["externalIds"]
paper_id = metadata["paperId"]
file_path = None
persist_dir = os.path.join(self.base_dir, f"{paper_id}.pdf")
if url and not os.path.exists(persist_dir):
# Download the document first
file_path = self._download_pdf(metadata["paperId"], url, persist_dir)
if (
not url
and externalIds
and "ArXiv" in externalIds
and not os.path.exists(persist_dir)
):
# download the pdf from arxiv
file_path = self._download_pdf_from_arxiv(
paper_id, externalIds["ArXiv"]
)
# Then, check if it's a valid PDF. If it's not, skip to the next document.
if file_path:
try:
pdf = PdfReader(open(file_path, "rb"))
except Exception as e:
logging.error(
f"Failed to read pdf with exception: {e}. Skipping document..."
)
continue
text = ""
for page in pdf.pages:
text += page.extract_text()
full_text_docs.append(Document(text=text, extra_info=metadata))
return full_text_docs
def _download_pdf_from_arxiv(self, paper_id, arxiv_id):
paper = next(self.arxiv.Search(id_list=[arxiv_id], max_results=1).results())
paper.download_pdf(dirpath=self.base_dir, filename=paper_id + ".pdf")
return os.path.join(self.base_dir, f"{paper_id}.pdf")
def load_data(
self,
query,
limit,
full_text=False,
returned_fields=[
"title",
"abstract",
"venue",
"year",
"paperId",
"citationCount",
"openAccessPdf",
"authors",
"externalIds",
],
) -> List[Document]:
"""
Loads data from Semantic Scholar based on the entered query and returned_fields.
Parameters
----------
query: str
The search query for the paper
limit: int, optional
The number of maximum results returned (default is 10)
returned_fields: list, optional
The list of fields to be returned from the search
Returns:
-------
list
The list of Document object that contains the search results
Raises:
------
Exception
If there is an error while performing the search
"""
try:
results = self.s2.search_paper(query, limit=limit, fields=returned_fields)
except (requests.HTTPError, requests.ConnectionError, requests.Timeout) as e:
logging.error(
"Failed to fetch data from Semantic Scholar with exception: %s", e
)
raise
except Exception as e:
logging.error("An unexpected error occurred: %s", e)
raise
documents = []
for item in results[:limit]:
openAccessPdf = getattr(item, "openAccessPdf", None)
abstract = getattr(item, "abstract", None)
title = getattr(item, "title", None)
text = None
# concat title and abstract
if abstract and title:
text = title + " " + abstract
elif not abstract:
text = title
metadata = {
"title": title,
"venue": getattr(item, "venue", None),
"year": getattr(item, "year", None),
"paperId": getattr(item, "paperId", None),
"citationCount": getattr(item, "citationCount", None),
"openAccessPdf": openAccessPdf.get("url") if openAccessPdf else None,
"authors": [author["name"] for author in getattr(item, "authors", [])],
"externalIds": getattr(item, "externalIds", None),
}
documents.append(Document(text=text, extra_info=metadata))
if full_text:
full_text_documents = self._get_full_text_docs(documents)
documents.extend(full_text_documents)
return documents
|