10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
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
|
