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Updated ejde parser format

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Fixed duplicate data dumping problem
Pushed new "ejde_buffer.zip"
This commit is contained in:
ldy 2023-11-02 04:28:06 +08:00
parent 50e30e105b
commit ad63bcf6c4
4 changed files with 130 additions and 74 deletions
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43
Parsers/00_Citation_spider/get_paper_citation.py
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@ -26,11 +26,12 @@ payload = {
jwt_token = jwt.encode(payload, secret_key, algorithm="HS256", headers=head) jwt_token = jwt.encode(payload, secret_key, algorithm="HS256", headers=head)
# Aminer API # Aminer API
api_get_id = "https://datacenter.aminer.cn/gateway/open_platform/api/v3/paper/list/by/publish" api_paper_id = "https://datacenter.aminer.cn/gateway/open_platform/api/v3/paper/list/by/publish"
api_get_citation = "https://datacenter.aminer.cn/gateway/open_platform/api/v3/paper/detail/list" api_paper_detail = "https://datacenter.aminer.cn/gateway/open_platform/api/v3/paper/detail/list"
api_author_id = "https://datacenter.aminer.cn/gateway/open_platform/api/v2/person/search"
def aminer_get_id(title): def aminer_get_paper_id(title):
headers = { headers = {
"Authorization": f"Bearer {jwt_token}" "Authorization": f"Bearer {jwt_token}"
} }
@ -39,7 +40,7 @@ def aminer_get_id(title):
"size": "", "size": "",
"title": re.sub(r'[^a-zA-Z0-9\s]+', ' ', title).strip() "title": re.sub(r'[^a-zA-Z0-9\s]+', ' ', title).strip()
} }
response = requests.get(api_get_id, headers=headers, params=params) response = requests.get(api_paper_id, headers=headers, params=params)
if response.status_code == 200: if response.status_code == 200:
data = response.json() data = response.json()
@ -49,7 +50,7 @@ def aminer_get_id(title):
not_on_aminer.append(title) not_on_aminer.append(title)
def aminer_post_citation(aminer_id): def aminer_post_paper_citation(aminer_id):
headers = { headers = {
"Content-Type": "application/json;charset=utf-8", "Content-Type": "application/json;charset=utf-8",
"Authorization": f"Bearer {jwt_token}" "Authorization": f"Bearer {jwt_token}"
@ -57,7 +58,7 @@ def aminer_post_citation(aminer_id):
request_data = { request_data = {
"ids": aminer_id "ids": aminer_id
} }
response = requests.post(api_get_citation, headers=headers, data=json.dumps(request_data)) response = requests.post(api_paper_detail, headers=headers, data=json.dumps(request_data))
if response.status_code == 200: if response.status_code == 200:
data = response.json() data = response.json()
@ -72,6 +73,31 @@ def aminer_post_citation(aminer_id):
aminer_paper_citation_retry.append(aminer_id) aminer_paper_citation_retry.append(aminer_id)
def aminer_author_info(author_aminer_id, author_name, offset):
headers = {
"Content-Type": "application/json;charset=utf-8",
"Authorization": f"Bearer {jwt_token}"
}
request_data = {
"ids": author_aminer_id,
"query": author_name,
"offset": offset
}
response = requests.post(api_paper_detail, headers=headers, data=json.dumps(request_data))
if response.status_code == 200:
data = response.json()
if data.get("success"):
for item in data.get('data', []):
if 'n_citation' in item:
n_citation = item['n_citation']
else:
n_citation = 0
aminer_paper_citation.append(n_citation)
else:
aminer_paper_citation_retry.append(author_aminer_id)
def scholarly_get_citation(title): def scholarly_get_citation(title):
# # Set up a ProxyGenerator object to use free proxies. This needs to be done only once per session # # Set up a ProxyGenerator object to use free proxies. This needs to be done only once per session
pg = ProxyGenerator() pg = ProxyGenerator()
@ -92,8 +118,7 @@ aminer_paper_citation = []
aminer_paper_citation_retry = [] aminer_paper_citation_retry = []
# scholarly_get_citation("Traveling waves for unbalanced bistable equations with density dependent diffusion") # scholarly_get_citation("Traveling waves for unbalanced bistable equations with density dependent diffusion")
aminer_get_paper_id("Heat kernel estimates for fourth-order non-uniformly elliptic operators with non-strongly convex symbols")
aminer_get_id("Heat kernel estimates for fourth-order non-uniformly elliptic operators with non-strongly convex symbols")
if aminer_paper_id: if aminer_paper_id:
aminer_post_citation(aminer_paper_id) aminer_post_paper_citation(aminer_paper_id)
print(aminer_paper_citation) print(aminer_paper_citation)

123
Parsers/01_EJDE_spider/ejde_main.py
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@ -1,7 +1,8 @@
import re
import time import time
import uuid import uuid
import requests import requests
import re import threading
import ejde_save import ejde_save
from retrying import retry from retrying import retry
@ -13,8 +14,8 @@ from concurrent.futures import ThreadPoolExecutor, as_completed
''' '''
爬取网站：'ejde.math.txstate.edu' 爬取网站：'ejde.math.txstate.edu'
Total number of papers: 2023/08/08 - 4761 Total number of papers: 2023/08/08 - 4785
Total Time via VPN w/100ms-delay: 306.73s Total Time via VPN w/100ms-delay: 48.04s
==========运行顺序========== ==========运行顺序==========
1、ejde_main 获取各年份的期刊链接 -> 抓取各篇论文的信息和作者信息 -> 调用ejde_save -> 存入小文件（json）暂存 1、ejde_main 获取各年份的期刊链接 -> 抓取各篇论文的信息和作者信息 -> 调用ejde_save -> 存入小文件（json）暂存
@ -23,6 +24,12 @@ from concurrent.futures import ThreadPoolExecutor, as_completed
''' '''
def save_data_thread_safe(data, data_lock, data_type):
with data_lock:
ejde_save.save_data(data, f"{data_type}", str(uuid.uuid4()) + ".json")
data.clear()
def datetime_transform(date): def datetime_transform(date):
month_typo = { month_typo = {
"Janaury": "January", "Janaury": "January",
@ -120,7 +127,7 @@ def process_html_article(baseweb, article):
# Get article title & url # Get article title & url
try: try:
title = article.text.strip() title = article.text.strip()
title = re.sub(r'\s+', ' ', title).strip() title = str(re.sub(r'\s+', ' ', title).strip())
article_url = baseweb + article.find_next("a")["href"] article_url = baseweb + article.find_next("a")["href"]
if "../../index.html" in article_url: if "../../index.html" in article_url:
print("Redundant URL:", article_url) print("Redundant URL:", article_url)
@ -162,11 +169,11 @@ def process_article(title, article_url):
# Extract title if title == None # Extract title if title == None
if not title: if not title:
title_match = re.search(r"<h3>(.*?)<p>", article_text) title_match = re.search(r"<h3>(.*?)<p>", article_text)
title = str(re.sub(r'<[^>]+>', '', title_match.group(1)).strip()) if title_match else None title = str(re.sub(r'<[^>]+>', '', title_match.group(1)).strip()) if title_match else ""
# Extract issue # Extract issue
issue_match = re.search(r'No\. (\d+)', article_text) issue_match = re.search(r'No\. (\d+)', article_text)
issue = issue_match.group(1) if issue_match else None issue = issue_match.group(1) if issue_match else ""
# Extract volume # Extract volume
volume_match = re.search(r'Vol\. (\d+)', article_text) volume_match = re.search(r'Vol\. (\d+)', article_text)
@ -189,21 +196,23 @@ def process_article(title, article_url):
volume = str(volume) volume = str(volume)
issue = "Conference " + str(issue_number) issue = "Conference " + str(issue_number)
else: else:
volume = None volume = ""
# Extract pp # Extract pp
pp_match = re.search(r'pp\. (\d+-\d+)', article_text) pp_match = re.search(r'pp\. (\d+-\d+)', article_text)
pp = pp_match.group(1) if pp_match else None pp = pp_match.group(1) if pp_match else ""
# Extract submission date # Extract submission date
match = re.search(r"Submitted ([A-Za-z]+\s+\d{1,2}, \d{4})", html) match = re.search(r"Submitted ([A-Za-z]+\s+\d{1,2}, \d{4})", html)
submitted_date = match.group(1) if match else None if not match:
match = re.search(r"Submitted\s+([A-Za-z]+\s+\d{1,2},\s+\d{4})", html)
submitted_date = match.group(1) if match else ""
if submitted_date: if submitted_date:
submitted_date = datetime_transform(submitted_date) submitted_date = datetime_transform(submitted_date)
# Extract publication date # Extract publication date
match = re.search(r"Published ([A-Za-z]+\s+\d{1,2}, \d{4})", html) match = re.search(r"Published ([A-Za-z]+\s+\d{1,2}, \d{4})", html)
publish_date = match.group(1) if match else None publish_date = match.group(1) if match else ""
if publish_date: if publish_date:
publish_date = datetime_transform(publish_date) publish_date = datetime_transform(publish_date)
@ -234,25 +243,25 @@ def process_article(title, article_url):
doi_match = re.search(r'DOI: ([^\t\n<]+)', html) doi_match = re.search(r'DOI: ([^\t\n<]+)', html)
if not doi_match: if not doi_match:
doi_match = re.search(r'DOI: (.+)', html) doi_match = re.search(r'DOI: (.+)', html)
doi = doi_match.group(1) if doi_match else None doi = doi_match.group(1) if doi_match else ""
doi = doi.replace('https://doi.org/', '') # strip doi website header
# Article_id # Article_id
article_id = str(uuid.uuid4()) article_id = str(uuid.uuid4())
# Author info # Author info
authors = [] authors = []
author_names = []
table = article_soup.find('table') table = article_soup.find('table')
if table: if table:
for row in table.find_all('tr'): for row in table.find_all('tr'):
cells = [cell.text.strip() for cell in row.find_all('td')] cells = [cell.text.strip() for cell in row.find_all('td')]
for cell in cells: for cell in cells:
if "email:" in cell: if "email" in cell:
cell = cell.split("email:") cell = cell.split("email")
email_list = str(cell[1]).split(',') email_list = str(cell[1]).split(',')
cell = cell[0] cell = cell[0]
elif "e-mail:" in cell: elif "e-mail" in cell:
cell = cell.split("e-mail:") cell = cell.split("e-mail")
email_list = str(cell[1]).split(',') email_list = str(cell[1]).split(',')
cell = cell[0] cell = cell[0]
else: else:
@ -264,8 +273,11 @@ def process_article(title, article_url):
# Data processing # Data processing
if cell[0]: if cell[0]:
authors.append(unidecode(cell[0])) author_id = str(uuid.uuid4())
name = re.split(r'[ .]', cell[0]) authors.append(author_id)
author_names.append(unidecode(cell[0]))
name = re.split(r'\s+', cell[0])
name = [item for item in name if item != '']
affiliation = ', '.join(cell[1:]).lstrip(",").rstrip(",").strip() affiliation = ', '.join(cell[1:]).lstrip(",").rstrip(",").strip()
affiliation = re.sub(r'^[^a-zA-Z]*', '', re.sub(r'\s+', ' ', re.sub(r',+', ',', affiliation))) affiliation = re.sub(r'^[^a-zA-Z]*', '', re.sub(r'\s+', ' ', re.sub(r',+', ',', affiliation)))
affiliation = affiliation.lstrip(",").rstrip(",").strip() affiliation = affiliation.lstrip(",").rstrip(",").strip()
@ -276,16 +288,19 @@ def process_article(title, article_url):
emails.append(unidecode(email_match.group())) if email_match else None emails.append(unidecode(email_match.group())) if email_match else None
author_data = { author_data = {
"author_id": str(uuid.uuid4()), "author_id": author_id,
"from_article": [article_id], "from_article": article_id,
"first_name": unidecode(name[0]), "first_name": unidecode(name[0]),
"last_name": unidecode(name[-1]), "last_name": unidecode(name[-1]),
"middle_name": unidecode(''.join(name[1:-1])) if len(name[1:-1]) > 0 else None, "middle_name": unidecode(''.join(name[1:-1])) if len(name[1:-1]) > 0 else "",
"affiliation": [{ "raw_name": unidecode(cell[0]),
"year": volume, "affiliation": [
"affiliation": unidecode(affiliation), {
"email": emails "year": volume,
}] "affiliation": unidecode(affiliation),
"email": ", ".join(emails)
}
]
} }
authorData.append(author_data) authorData.append(author_data)
authorNum += 1 authorNum += 1
@ -308,12 +323,12 @@ def process_article(title, article_url):
matches = matches.replace('["', '').replace('"]', '').replace('[\'', '').replace('\']', '') matches = matches.replace('["', '').replace('"]', '').replace('[\'', '').replace('\']', '')
matches = matches.split("<p>") matches = matches.split("<p>")
for match in matches: for match in matches:
if "email:" in match: if "email" in match:
match = match.split("email:") match = match.split("email")
email_list = str(match[1]).split(',') email_list = str(match[1]).split(',')
match = match[0] match = match[0]
elif "e-mail:" in match: elif "e-mail" in match:
match = match.split("e-mail:") match = match.split("e-mail")
email_list = str(match[1]).split(',') email_list = str(match[1]).split(',')
match = match[0] match = match[0]
else: else:
@ -330,8 +345,11 @@ def process_article(title, article_url):
# Data processing # Data processing
if match[0]: if match[0]:
author_id = str(uuid.uuid4())
authors.append(author_id)
authors.append(unidecode(match[0])) authors.append(unidecode(match[0]))
name = re.split(r'[ .]', match[0]) name = re.split(r'\s+', match[0])
name = [item for item in name if item != '']
affiliation = ''.join(match[1:]).lstrip(",").rstrip(",").strip() affiliation = ''.join(match[1:]).lstrip(",").rstrip(",").strip()
affiliation = re.sub(r'^[^a-zA-Z]*', '', re.sub(r'\s+', ' ', re.sub(r',+', ',', affiliation))) affiliation = re.sub(r'^[^a-zA-Z]*', '', re.sub(r'\s+', ' ', re.sub(r',+', ',', affiliation)))
affiliation = affiliation.lstrip(",").rstrip(",").strip() affiliation = affiliation.lstrip(",").rstrip(",").strip()
@ -342,16 +360,19 @@ def process_article(title, article_url):
emails.append(unidecode(email_match.group())) if email_match else None emails.append(unidecode(email_match.group())) if email_match else None
author_data = { author_data = {
"author_id": str(uuid.uuid4()), "author_id": author_id,
"from_article": [article_id], "from_article": article_id,
"first_name": unidecode(name[0]), "first_name": unidecode(name[0]),
"last_name": unidecode(name[-1]), "last_name": unidecode(name[-1]),
"middle_name": unidecode(''.join(name[1:-1])) if len(name[1:-1]) > 0 else None, "middle_name": unidecode(''.join(name[1:-1])) if len(name[1:-1]) > 0 else "",
"affiliation": [{ "raw_name": unidecode(match[0]),
"year": volume, "affiliation": [
"affiliation": unidecode(affiliation), {
"email": emails "year": volume,
}] "affiliation": unidecode(affiliation),
"email": ", ".join(emails)
}
]
} }
authorData.append(author_data) authorData.append(author_data)
authorNum += 1 authorNum += 1
@ -368,7 +389,7 @@ def process_article(title, article_url):
"article_id": article_id, "article_id": article_id,
"title": unidecode(title), "title": unidecode(title),
"authors": authors, "authors": authors,
"corresponding_authors": None, "author_names": author_names,
"submit_datetime": submitted_date, "submit_datetime": submitted_date,
"publish_datetime": publish_date, "publish_datetime": publish_date,
"keywords": keywords, "keywords": keywords,
@ -386,12 +407,10 @@ def process_article(title, article_url):
# Save the data periodically based on batch size # Save the data periodically based on batch size
if len(articleData) % batch_size == 0: if len(articleData) % batch_size == 0:
ejde_save.save_data(articleData, "Article_TS", str(uuid.uuid4()) + ".json") save_data_thread_safe(articleData, articleDataLock, "Article_TS")
articleData.clear()
if len(authorData) % batch_size == 0: if len(authorData) % batch_size == 0:
ejde_save.save_data(authorData, "Author_TS", str(uuid.uuid4()) + ".json") save_data_thread_safe(authorData, authorDataLock, "Author_TS")
authorData.clear()
start_time = time.time() start_time = time.time()
@ -429,6 +448,8 @@ authorNum = 0
articleNum = 0 articleNum = 0
batch_size = 100 # Number of articles to process before saving batch_size = 100 # Number of articles to process before saving
authorDataLock = threading.Lock()
articleDataLock = threading.Lock()
executor = ThreadPoolExecutor(max_workers=int(len(url_list) / 2)) # Set the number of worker threads executor = ThreadPoolExecutor(max_workers=int(len(url_list) / 2)) # Set the number of worker threads
# Process each URL using multithreading # Process each URL using multithreading
@ -444,9 +465,9 @@ for future in as_completed(futures):
# Retry failed processing paper # Retry failed processing paper
print("START RETRYING:", len(failedData)) print("START RETRYING:", len(failedData))
while failedData: while failedData:
data = failedData.pop(0) fail_data = failedData.pop(0)
articleTitle = data["title"] articleTitle = fail_data["title"]
articleUrl = data["URL"] articleUrl = fail_data["URL"]
try: try:
process_article(articleTitle, articleUrl) process_article(articleTitle, articleUrl)
except Exception as retry_err: except Exception as retry_err:
@ -460,11 +481,11 @@ while failedData:
# Save remaining data # Save remaining data
if len(articleData) > 0: if len(articleData) > 0:
ejde_save.save_data(articleData, "Article_TS", str(uuid.uuid4()) + ".json") ejde_save.save_data(articleData, "Article_TS", str(uuid.uuid4()) + ".json")
print("COMPLETE: All EJDE article data has been saved to ./ejde_buffer/Article_TS/") print("COMPLETE: All EJDE article data has been saved to ./ejde_buffer/Article_TS/")
if len(authorData) > 0: if len(authorData) > 0:
ejde_save.save_data(authorData, "Author_TS", str(uuid.uuid4()) + ".json") ejde_save.save_data(authorData, "Author_TS", str(uuid.uuid4()) + ".json")
print("COMPLETE: All EJDE author data has been saved to ./ejde_buffer/Author_TS/") print("COMPLETE: All EJDE author data has been saved to ./ejde_buffer/Author_TS/")
# Save error record # Save error record
if len(totallyFailedData) > 0: if len(totallyFailedData) > 0:
@ -485,5 +506,5 @@ print("Total fetched author:", authorNum)
print("time elapsed: {:.2f}s".format(time.time() - start_time)) print("time elapsed: {:.2f}s".format(time.time() - start_time))
# Transfer to large file and delete the temporary storage files # Transfer to large file and delete the temporary storage files
ejde_save.Transf() ejde_save.transform_data()
ejde_save.delete() # ejde_save.delete_data()

38
Parsers/01_EJDE_spider/ejde_save.py
View File

@ -14,8 +14,8 @@ def save_data(dataset, filetype, filename):
# Write into output files # Write into output files
def Transf(): def transform_data():
def Read(folder_path, output_files): def read(folder_path, output_files):
# Create new folders # Create new folders
os.makedirs('./ejde_buffer/Article_output/', exist_ok=True) os.makedirs('./ejde_buffer/Article_output/', exist_ok=True)
os.makedirs('./ejde_buffer/Author_output/', exist_ok=True) os.makedirs('./ejde_buffer/Author_output/', exist_ok=True)
@ -24,6 +24,8 @@ def Transf():
data_2010_2014 = [] data_2010_2014 = []
data_2015_2020 = [] data_2015_2020 = []
data_newest = [] data_newest = []
data_no_date = []
data_integrate = []
for filename in os.listdir(folder_path): for filename in os.listdir(folder_path):
if filename.endswith('.json'): if filename.endswith('.json'):
@ -31,24 +33,29 @@ def Transf():
with open(file_path, 'r', encoding='utf-8') as file: with open(file_path, 'r', encoding='utf-8') as file:
data = json.load(file) data = json.load(file)
for Dict in data: for Dict in data:
if Dict.get('volume') is not None or Dict.get('affiliation', [{}])[0].get('year', 0) is not None: if Dict.get('volume') is not None or Dict.get('affiliation', [{}])[0].get('year', 0) != '':
# Select data # Select data
if int(Dict.get('volume') or Dict.get('affiliation', [{}])[0].get('year', 0)) <= 2009: if int(Dict.get('volume') or Dict.get('affiliation', [{}])[0].get('year', 0)) <= 2009:
data_oldest.append(Dict) data_oldest.append(Dict)
elif int(Dict.get('volume') or Dict.get('affiliation', [{}])[0].get('year', 0)) <= 2014: elif int(Dict.get('volume') or Dict.get('affiliation', [{}])[0].get('year', 0)) <= 2014:
data_2010_2014.append(Dict) data_2010_2014.append(Dict)
elif int(Dict.get('volume') or Dict.get('affiliation', [{}])[0].get('year', 0)) <= 2020: elif int(Dict.get('volume') or Dict.get('affiliation', [{}])[0].get('year', 0)) <= 2020:
data_2015_2020.append(Dict) data_2015_2020.append(Dict)
else: else:
data_newest.append(Dict) data_newest.append(Dict)
else:
data_no_date.append(Dict)
data_integrate.append(data_oldest)
data_integrate.append(data_2010_2014)
data_integrate.append(data_2015_2020)
data_integrate.append(data_newest)
data_integrate.append(data_no_date)
# Transfer # Transfer
Data = [data_oldest, data_2010_2014, data_2015_2020, data_newest] Data = [data_oldest, data_2010_2014, data_2015_2020, data_newest, data_no_date, data_integrate]
for index in range(0, 4): for index in range(0, 6):
with open(output_files[index], 'w', encoding='utf-8') as file: with open(output_files[index], 'w', encoding='utf-8') as file:
json.dump(Data[index], file, indent=4) json.dump(Data[index], file, indent=4)
@ -61,26 +68,30 @@ def Transf():
'./ejde_buffer/Author_output/EJDE_Author_output_file(oldest).json', './ejde_buffer/Author_output/EJDE_Author_output_file(oldest).json',
'./ejde_buffer/Author_output/EJDE_Author_output_file(2010-2014).json', './ejde_buffer/Author_output/EJDE_Author_output_file(2010-2014).json',
'./ejde_buffer/Author_output/EJDE_Author_output_file(2015-2020).json', './ejde_buffer/Author_output/EJDE_Author_output_file(2015-2020).json',
'./ejde_buffer/Author_output/EJDE_Author_output_file(newest).json' './ejde_buffer/Author_output/EJDE_Author_output_file(newest).json',
'./ejde_buffer/Author_output/EJDE_Author_output_file(no date).json',
'./ejde_buffer/Author_output/EJDE_Author_output_file(integration).json'
] ]
article_output_file = [ article_output_file = [
'./ejde_buffer/Article_output/EJDE_Article_output_file(oldest).json', './ejde_buffer/Article_output/EJDE_Article_output_file(oldest).json',
'./ejde_buffer/Article_output/EJDE_Article_output_file(2010-2014).json', './ejde_buffer/Article_output/EJDE_Article_output_file(2010-2014).json',
'./ejde_buffer/Article_output/EJDE_Article_output_file(2015-2020).json', './ejde_buffer/Article_output/EJDE_Article_output_file(2015-2020).json',
'./ejde_buffer/Article_output/EJDE_Article_output_file(newest).json' './ejde_buffer/Article_output/EJDE_Article_output_file(newest).json',
'./ejde_buffer/Article_output/EJDE_Article_output_file(no date).json',
'./ejde_buffer/Article_output/EJDE_Article_output_file(integration).json'
] ]
# Read and write into files # Read and write into files
Read(author_folder_path, author_output_file) read(author_folder_path, author_output_file)
Read(article_folder_path, article_output_file) read(article_folder_path, article_output_file)
# End # End
print("\nData has been written into files.") print("\nData has been written into files.")
# Delete files in temporary storage area # Delete files in temporary storage area
def delete(): def delete_data():
folder_paths = ['./ejde_buffer/Author_TS', './ejde_buffer/Article_TS'] folder_paths = ['./ejde_buffer/Author_TS', './ejde_buffer/Article_TS']
for folder_path in folder_paths: for folder_path in folder_paths:
file_names = os.listdir(folder_path) file_names = os.listdir(folder_path)
@ -89,5 +100,4 @@ def delete():
if os.path.isfile(file_path): if os.path.isfile(file_path):
os.remove(file_path) os.remove(file_path)
os.rmdir(folder_path) os.rmdir(folder_path)
print('\nAttention: The temporary storage files have been deleted!') print('\nAttention: The temporary storage files have been deleted!')