def get_captcha(session, captcha_url):
resp = WebRequest.get_response(captcha_url, session=session)
im = Image.open(io.BytesIO(resp.content))
im = im.convert('RGB')
pixdata = im.load()
weight, height = im.size
for x in range(weight):
for y in range(height):
rgb = pixdata[x, y]
if (rgb[0] - rgb[1] > 73) and (rgb[0] - rgb[2] > 73):
pixdata[x, y] = (0, 0, 0)
else:
pixdata[x, y] = (255, 255, 255)
captcha = pytesseract.image_to_string(im).strip()
if len(captcha) != 4:
return get_captcha(session, captcha_url)
payload = util.query_payload(tryCode=captcha)
funding_url = 'http://output.nsfc.gov.cn/baseQuery/data/supportQueryResultsData'
resp = WebRequest.get_response(funding_url,
method='POST',
session=session,
json=payload)
if resp.json()['message'] != '验证码错误':
click.secho('right captcha: {}'.format(captcha), fg='green', bold=True)
return captcha
click.secho('wrong captcha: {}'.format(captcha), fg='yellow')
return get_captcha(session, captcha_url)
def deal_captcha(self, url, outdir, filename, chunk_size):
"""deal with the captcha
"""
soup = WR.get_soup(url)
img = soup.select_one('#captcha').attrs['src']
img_url = url.rsplit('/', 3)[0] + img
# print(img_url)
self.logger.warning(f'need to type in the captcha: {img_url}')
if os.getenv('DISPLAY'):
self.logger.info(
f'failed to open the picture, you can open it in your browser: {img_url}'
)
else:
content = WR.get_response(img_url, max_try=1).content
im = Image.open(io.BytesIO(content))
# im.show() # this will block the program
im.save('tmp.png')
# ****************************
# ***** non-blocked mode *****
# ****************************
pylab.ion()
img = pylab.imread('tmp.png')
pylab.imshow(img)
pylab.show()
while True:
answer = click.prompt('please input the captcha')
if answer == 'new':
return self.download(url,
outdir=outdir,
filename=filename,
chunk_size=chunk_size)
payload = {
'id': img_url.split('/')[-1].split('.')[0],
'answer': answer
}
# payload = {'id': '6058249282282', 'answer': 'manila'}
self.logger.debug(payload)
resp = WR.get_response(url,
method='POST',
stream=True,
data=payload)
if resp.headers['Content-Type'] == 'application/pdf':
pylab.close()
return resp
self.logger.warning('bad captcha, try again!')
def do_search(self, url, requires, **kwargs):
"""
"""
if not kwargs.get('ratifyNo'):
for key, name in requires.items():
if not kwargs.get(key):
kwargs[key] = click.prompt('请输入{}'.format(name))
payload = util.query_payload(**kwargs)
data = WebRequest.get_response(url, method='POST', json=payload, session=self.session, max_try=20).json()
if data['code'] != 200:
print(payload)
click.secho('error code: {}'.format(json.dumps(data, ensure_ascii=False)), fg='red')
exit()
for each in self.do_search(url, requires, **payload):
yield each
else:
yield data
# 结果大于10条
total = data['data']['iTotalRecords']
if (payload['pageNum'] + 1) * payload['pageSize'] < total:
payload['pageNum'] += 1
click.secho('>>> crawling {code}-{projectType}-{ratifyYear} page {page} ...'.format(page=payload['pageNum'] + 1, **payload), fg='cyan')
for each in self.do_search(url, requires, **payload):
yield each
def get_field_codes(cls):
"""
所有的学科代码
"""
url = cls.base_url + '/common/data/fieldCode'
print(url)
return WR.get_response(url).json()['data']
def elink(self, ids, dbfrom='pubmed', cmd='neighbor', **kwargs):
"""
https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ELink
> - get cited (`{"linkname": "pubmed_pubmed_citedin"}`)
>> elink.fcgi?dbfrom=pubmed&db=pubmed&id=20210808&cmd=neighbor&retmode=json
> - get pdf url
>> elink.fcgi?dbfrom=pubmed&db=pubmed&cmd=prlinks&id=10210801
cmds:
- neighbor (default)
- neighbor_score
- neighbor_history
- acheck
- ncheck
- lcheck
- llinks
- llinkslib
- prlinks
"""
url = self.base_url + 'elink.fcgi'
params = self.parse_params(retmode='json',
id=ids,
dbfrom=dbfrom,
cmd=cmd,
**kwargs)
result = WebRequest.get_response(url, params=params).json()
return result
def conclusion_project(self, projectid):
"""
结题项目详情
"""
url = self.base_url + '/baseQuery/data/conclusionProjectInfo/' + projectid
data = WebRequest.get_response(url).json()['data']
return data
def support_types(self):
"""
资助类别
"""
# url = self.base_url + '/common/data/supportTypeData' # 包含子类
url = self.base_url + '/common/data/supportTypeClassOneData' # 仅一类
return WebRequest.get_response(url).json()['data']
def get_mim2gene(self, outfile=None):
url = self.omim_url + '/static/omim/data/mim2gene.txt'
resp = WR.get_response(url, stream=True)
if outfile:
with open(outfile, 'wb') as out:
for chunk in resp.iter_content(chunk_size=512):
out.write(chunk)
self.logger.debug(f'save file: {outfile}')
else:
return resp.text
def list_provinces(self):
"""省份列表
"""
self.logger.debug('list provinces ...')
soup = WR.get_soup(self.index_url)
province_list = [
each.attrs['value']
for each in soup.select('#province_main option[value!=""]')
]
return province_list
def search(self, term, max_try=3):
"""
term: URL, PMID, DOI or search string
return: the url of pdf
"""
soup = WR.get_soup(self.url)
form = soup.select_one('form[method="POST"]')
post_url = self.url if form.attrs['action'] == '/' else form.attrs[
'action']
payload = {'sci-hub-plugin-check': '', 'request': term}
self.logger.debug(f'search pdf url for: {term}')
while max_try:
max_try -= 1
soup = WR.get_soup(post_url,
method='POST',
data=payload,
timeout=self.timeout)
pdf = soup.select_one('#pdf')
if 'article not found' in soup.text:
self.logger.warning(f'article not found [{term}]')
return
elif not pdf:
# print(soup.select('title'))
continue
pdf_url = pdf.attrs['src']
if pdf_url.startswith('//'):
pdf_url = post_url.split(':')[0] + f':{pdf_url}'
self.logger.info(f'pdf url: {pdf_url}')
return pdf_url
self.logger.error(
f'your searching has no result, please check! [{term}]')
def get_conclusion_report_images(cls, projectid):
url = cls.base_url + '/baseQuery/data/completeProjectReport'
index = 1
while True:
payload = {'id': projectid, 'index': index}
res = WR.get_response(url, method='POST',
data=payload).json()['data']
if not res['hasnext']:
break
yield cls.base_url + res['url']
index += 1
def fetch_factor(*kws):
for kw in kws:
url = BASE_URL + kw
resp = WebRequest.get_response(url)
soup = WebRequest.get_soup(resp)
context = {}
trs = soup.select('table tr')
if len(trs) > 2:
print('multiple result for kw: {}'.format(kw))
elif len(trs) < 2:
print('no result for kw: {}'.format(kw))
else:
title = [th.text for th in trs[0].find_all('th')[2:]]
values = [td.text for td in trs[1].find_all('td')[2:]]
if values[-1]:
context['factor_history'] = json.dumps(dict(zip(title,
values)))
context['factor'] = values[-1]
context['kw'] = kw
if context:
return context
def download(self,
url,
outdir='.',
filename=None,
chunk_size=512,
overwrite=None,
show_progress=True):
"""download pdf from url
"""
filename = filename or os.path.basename(url).split('#')[0]
if outdir != '.' and not os.path.exists(outdir):
os.makedirs(outdir)
outfile = os.path.join(outdir, filename)
if os.path.isfile(outfile) and os.stat(outfile).st_size > 0:
if not isinstance(overwrite, bool):
overwrite = click.confirm(
'The file already exists, do you want to overwrite it?')
if overwrite:
self.logger.debug(f'overwriting the file: {outfile}')
else:
self.logger.debug(f'skip downloading file: {outfile}')
return True
resp = WR.get_response(url, stream=True)
if resp.headers['Content-Type'] != 'application/pdf':
resp = self.deal_captcha(url, outdir, filename, chunk_size)
length = int(resp.headers.get('Content-Length'))
# if os.path.isfile(outfile) and os.stat(outfile).st_size == length:
self.logger.info(
f'downloading pdf: {outfile} [{length/1024/1024:.2f} M]')
bar = click.progressbar(length=length,
label='downloading',
show_percent=True,
show_pos=True,
show_eta=True)
with open(outfile, 'wb') as out, bar:
for chunk in resp.iter_content(chunk_size=chunk_size):
out.write(chunk)
if show_progress:
bar.update(chunk_size)
self.logger.info(f'save file: {outfile}')
return True
def einfo(self, **kwargs):
"""
https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EInfo
> - show all database list
>> einfo.fcgi?db=
> - show dbinfo for given database
>> einfo.fcgi?db=pubmed
"""
url = self.base_url + 'einfo.fcgi'
params = self.parse_params(retmode='json', **kwargs)
info = WebRequest.get_response(url,
params=params,
allowed_codes=[200, 400]).json()
return info
def check_host():
"""
checking available urls of Sci-Hub
"""
url = 'https://lovescihub.wordpress.com/'
soup = WR.get_soup(url)
text = soup.select_one('.entry-content p:nth-child(2)').text
update_text = soup.select_one('.entry-title').text
update_time = date_parse(
re.findall(r'Last check time:(.+?)\)', update_text)[0])
hosts = dict(re.findall(r'(http.+?)\s+(.+?s)', text))
return hosts, update_time
def list_support_types(self):
"""项目类别列表
Bug: 网页显示：应急管理项目
实际应该：科学部主任基金项目/应急管理项目
"""
self.logger.debug('list support types ...')
soup = WR.get_soup(self.index_url)
subcategory_list = []
for option in soup.select('select#subcategory option')[1:]:
if option.text == '应急管理项目':
text = '科学部主任基金项目/应急管理项目'
else:
text = option.text
subcategory_list.append(text)
return subcategory_list
def search_page(self, params, payload):
"""查询页面
"""
self.logger.debug(
f'searching for: {payload} [page: {params["currentpage"]}]')
while True:
soup = WR.get_soup(self.search_url,
method='POST',
params=params,
data=payload)
if not soup.select_one('#dict div b'):
self.logger.warning(f'{soup.text}')
if '需要先注册登录' in soup.text:
exit()
time.sleep(30)
continue
time.sleep(random.randint(5, 10))
return soup
def get_conclusion_data(cls, ratify_number, detail=True):
"""
获取指定项目批准号的结题数据
"""
url = cls.base_url + '/baseQuery/data/conclusionQueryResultsData'
payload = {
'ratifyNo': ratify_number,
'queryType': 'input',
'complete': 'true',
}
result = WR.get_response(url, method='POST',
json=payload).json()['data']['resultsData']
data = {}
if result:
data['projectid'] = result[0][0]
data['project_type'] = result[0][3]
data['result_stat'] = result[0][10]
if detail and data.get('projectid'):
detail_data = cls.get_detail_data(data['projectid'])
data.update(detail_data)
return data
def get_conclusion_report(cls,
ratify_number,
tmpdir='tmp',
pdf=True,
outfile=None):
data = cls.get_conclusion_data(ratify_number, detail=False)
if not data:
cls.logger.warning(f'no conclusion result for: {ratify_number}')
return
images = list(cls.get_conclusion_report_images(data['projectid']))
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
pngs = []
for n, url in enumerate(images, 1):
name = os.path.basename(url)
png = f'{tmpdir}/{name}.png'
pngs.append(png)
cls.logger.debug(
f'[{n}/{len(images)}] download png: {url} => {png}')
resp = WR.get_response(url, stream=True)
with open(png, 'wb') as out:
for chunk in resp.iter_content(chunk_size=512):
out.write(chunk)
cls.logger.debug(f'save png: {png}')
if pdf:
cls.logger.debug('converting *png to pdf')
outfile = outfile or f'{ratify_number}.pdf'
with open(outfile, 'wb') as out:
out.write(img2pdf.convert(pngs))
size = human_readable.file_size(os.stat(outfile).st_size)
cls.logger.info(f'save pdf: {outfile} [{size}]')
return True
def efetch(self, ids, batch_size=5, **kwargs):
"""
https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
> - fetch from a database for given ids
>> efetch.cgi?db=pubmed&id=1,2,3
"""
url = self.base_url + 'efetch.fcgi'
self.logger.info('fetching start: total {}, batch_size: {}'.format(
len(ids), batch_size))
for n in range(0, len(ids), batch_size):
_id = ','.join(ids[n:n + batch_size])
self.logger.debug(f'fetching xml: {n+1} - {n+batch_size}')
params = self.parse_params(id=_id, retmode='xml')
xml = WebRequest.get_response(url, params=params).text
self.logger.debug(f'parsing xml: {n+1} - {n+batch_size}')
for context in xml_parser.parse(xml):
article = Article(**context)
yield article
def list_codes(self):
self.logger.debug('list subject codes ...')
url = self.base_url + '/js/nsfctags2019multiple.js'
resp = WR.get_response(url)
codes = defaultdict(list)
for line in resp.text.split('\n'):
if line.startswith('subtag['):
linelist = line.strip().split("', '")
subject = linelist[2] # 学部
code1 = linelist[3] # 一级学科 A01
code2 = linelist[4] # 二级学科 A0101
code3 = linelist[5] # 二级学科 A010101
# name = linelist[6].split("'")[0] # 学科名字
if code1 not in codes[subject]:
codes[subject].append(code1)
if code2 not in codes[code1]:
codes[code1].append(code2)
if code3 not in codes[code2]:
codes[code2].append(code3)
# print(subject, name, code1, code2, code3)
return dict(codes)
def field_codes(self):
"""
申请代码
"""
url = self.base_url + '/common/data/fieldCode'
return WebRequest.get_response(url).json()['data']
context['author_first'] = context['author_last'] = '.'
if authors:
context['author_first'] = authors[0]
if len(authors) > 1:
context['author_last'] = authors[-1]
context['authors'] = ',\n'.join(author_list)
context['pub_types'] = Article.xpath(
'PublicationTypeList/PublicationType/text()')
context['doi'] = PubmedArticle.findtext(
'PubmedData/ArticleIdList/ArticleId[@IdType="doi"]')
context['pmc'] = PubmedArticle.findtext(
'PubmedData/ArticleIdList/ArticleId[@IdType="pmc"]')
yield context
if __name__ == '__main__':
import json
from webrequests import WebRequest
pmid = '17284678,9997'
pmid = '28143587'
pmid = '33577981'
url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={pmid}&retmode=xml'
resp = WebRequest.get_response(url)
for context in parse(resp.text):
print(json.dumps(context, indent=2))
def esearch(self,
term,
retstart=0,
retmax=250,
head=False,
limit=None,
**kwargs):
"""
https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
> -search from a database from given term
>> - esearch.cgi?db=pubmed&term=ngs
>> - esearch.cgi?db=pubmed&term=ngs&retmode=xml&field=TIAB
>> - esearch.cgi?db=pubmed&term=ngs[Title/Abstract]&retmode=xml
"""
url = self.base_url + 'esearch.fcgi'
params = self.parse_params(term=term,
retmode='json',
retstart=retstart,
retmax=retmax,
**kwargs)
# print(params)
result = WebRequest.get_response(url,
params=params).json()['esearchresult']
if head:
return result
self.logger.info(
'{count} articles found with term: {querytranslation}'.format(
**result))
if limit is None and int(result['count']) > 250:
self.logger.warning(
'too many results, you can limit output with option "-l/--limit N", '
'or simplify your input with sub-command "advance-search" ')
exit(1)
idlist = result['idlist']
while int(result['retstart']) + int(result['retmax']) < int(
result['count']):
if limit and len(idlist) >= limit:
break
retstart = int(result['retstart']) + int(result['retmax'])
params = self.parse_params(term=term,
retmode='json',
retstart=retstart,
retmax=retmax,
**kwargs)
result = WebRequest.get_response(
url, params=params).json()['esearchresult']
idlist += result['idlist']
if limit:
self.logger.info('limit {} from {}'.format(limit, result['count']))
idlist = idlist[:limit]
if idlist:
self.logger.debug('idlist: {} ...'.format(', '.join(idlist[:10])))
else:
self.logger.warning('no result for term: {}'.format(term))
return idlist
def get_soup(self, url):
soup = WR.get_soup(url)
return soup
def list_projects(cls):
soup = WR.get_soup(cls.url)
for box in soup.select('.input-area .ms-checkbox input'):
yield box.attrs['value']
class Official(object):
base_url = 'http://output.nsfc.gov.cn'
logger = SimpleLogger('Official')
field_codes = WR.get_response(base_url +
'/common/data/fieldCode').json()['data']
@classmethod
def get_field_codes(cls):
"""
所有的学科代码
"""
url = cls.base_url + '/common/data/fieldCode'
print(url)
return WR.get_response(url).json()['data']
@classmethod
def list_root_codes(cls):
"""
获取所有的学科分类代码
"""
root_codes = {}
for context in cls.field_codes:
if len(context['code']) == 1:
root_codes[context['code']] = context['name']
return root_codes
@classmethod
def list_child_codes(cls, keys):
"""
获取最低级的学科代码
C01 --> C010101, C010102, ...
H10 --> H1001, H1002, ...
"""
child_codes = {}
for key in keys.split(','):
for context in cls.field_codes:
code = context['code']
if len(code) == 1:
continue
if code.startswith(key):
child_codes[code] = context['name']
if code[:-2] in child_codes:
del child_codes[code[:-2]]
return child_codes
@classmethod
def get_conclusion_data(cls, ratify_number, detail=True):
"""
获取指定项目批准号的结题数据
"""
url = cls.base_url + '/baseQuery/data/conclusionQueryResultsData'
payload = {
'ratifyNo': ratify_number,
'queryType': 'input',
'complete': 'true',
}
result = WR.get_response(url, method='POST',
json=payload).json()['data']['resultsData']
data = {}
if result:
data['projectid'] = result[0][0]
data['project_type'] = result[0][3]
data['result_stat'] = result[0][10]
if detail and data.get('projectid'):
detail_data = cls.get_detail_data(data['projectid'])
data.update(detail_data)
return data
@classmethod
def get_detail_data(cls, projectid):
url = cls.base_url + '/baseQuery/data/conclusionProjectInfo/' + projectid
data = WR.get_response(url).json()['data']
return data
@classmethod
def get_conclusion_report(cls,
ratify_number,
tmpdir='tmp',
pdf=True,
outfile=None):
data = cls.get_conclusion_data(ratify_number, detail=False)
if not data:
cls.logger.warning(f'no conclusion result for: {ratify_number}')
return
images = list(cls.get_conclusion_report_images(data['projectid']))
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
pngs = []
for n, url in enumerate(images, 1):
name = os.path.basename(url)
png = f'{tmpdir}/{name}.png'
pngs.append(png)
cls.logger.debug(
f'[{n}/{len(images)}] download png: {url} => {png}')
resp = WR.get_response(url, stream=True)
with open(png, 'wb') as out:
for chunk in resp.iter_content(chunk_size=512):
out.write(chunk)
cls.logger.debug(f'save png: {png}')
if pdf:
cls.logger.debug('converting *png to pdf')
outfile = outfile or f'{ratify_number}.pdf'
with open(outfile, 'wb') as out:
out.write(img2pdf.convert(pngs))
size = human_readable.file_size(os.stat(outfile).st_size)
cls.logger.info(f'save pdf: {outfile} [{size}]')
return True
@classmethod
def get_conclusion_report_images(cls, projectid):
url = cls.base_url + '/baseQuery/data/completeProjectReport'
index = 1
while True:
payload = {'id': projectid, 'index': index}
res = WR.get_response(url, method='POST',
data=payload).json()['data']
if not res['hasnext']:
break
yield cls.base_url + res['url']
index += 1
def get_detail_data(cls, projectid):
url = cls.base_url + '/baseQuery/data/conclusionProjectInfo/' + projectid
data = WR.get_response(url).json()['data']
return data
def ncbi_citations(pmid, fmt=None):
url = 'https://pubmed.ncbi.nlm.nih.gov/{}/citations/'.format(pmid)
data = WebRequest.get_response(url).json()
if fmt in data:
return data[fmt]
return data
def get_detail(cls, url):
soup = WR.get_soup(url)
for column in soup.select('.journal-content .journal-content-column'):
key = column.select_one('.column-label').text
value = column.select_one('.font-black').text.strip()
yield key, value
