def index(self):
"""
By Default Flask will come into this when we run the file.
* The can be accessed by 125.0.0.5000/api?doi=
* User can either search for a particular doi or can get all the data available in the database
"""
if 'doi' in request.args:
global doi_s
doi_s = str(request.args['doi'])
else:
return 'Error:'
global out_db
if doi_s == 'all':
out_db = database.read_all()
return redirect(url_for('ApiView:display_all'))
try:
doi.validate_doi(doi_s)
domain = doi.get_real_url_from_doi(doi_s)
except ValueError:
return 'Invalid doi'
doi_temp = database.check([doi_s])
if doi_temp:
scrap = scrape.Scrape()
scrap.scrape([domain], current_app.config['DICT_OF_SPIDERS'])
out_db = database.read([doi_s])
return redirect(url_for('ApiView:display_all'))
def main(f, failed_out, new_out, log_out):
logging.basicConfig(filename=log_out, level=logging.INFO)
logging.getLogger().addHandler(logging.StreamHandler())
new_docs = []
failed_docs = []
try:
with open(f) as fd:
docs = list(yaml.load_all(fd))
N = len(docs)
for K, d in enumerate(docs):
affs = has_affiliation(d)
success_rate = 100.0 - float(len(failed_docs)) / N * 100
if affs:
new_docs.append(d)
continue
try:
url = doi.get_real_url_from_doi(d['doi'])
logging.info(
"{c.Fore.CYAN}[{s:.1f}%]: {K}/{N}. {t}>>"
"{c.Fore.YELLOW}Trying {0}{c.Style.RESET_ALL}"
.format(url, s=success_rate,
K=K, N=N, t=time.ctime(), c=colorama))
downs = papis.downloaders.get_matching_downloaders(url)
downs[0].fetch_data()
ctx = downs[0].ctx
affs = has_affiliation(ctx.data)
if affs:
d['author_list'] = ctx.data['author_list']
else:
raise Exception('No affiliations')
except Exception as e:
d['_error_msg'] = str(e)
logging.info("{c.Fore.RED}\tFailed ({e}){c.Style.RESET_ALL}"
.format(e=e, c=colorama))
failed_docs.append(d)
else:
logging.info("{c.Fore.GREEN}\tsuccess "
"{affs!s:.100}{c.Style.RESET_ALL}"
.format(url, affs=affs, c=colorama))
new_docs.append(d)
except Exception as e:
logging.error(e)
finally:
with open(failed_out, 'w+') as fd:
logging.info('writing ' + failed_out)
yaml.dump_all(
list(failed_docs),
fd,
allow_unicode=True,
default_flow_style=False)
with open(new_out, 'w+') as fd:
logging.info('writing '+ new_out)
yaml.dump_all(
list(new_docs),
fd,
allow_unicode=True,
default_flow_style=False)
def test_get_real_url_from_doi() -> None:
data = [
('10.1016/S0009-2614(97)04014-1',
'https://www.sciencedirect.com/science/'
'article/abs/pii/S0009261497040141'),
]
for doi, url in data:
assert url == get_real_url_from_doi(doi)
def search_doi(self):
"""
Get Input from the user , validate and return the bibliographical details
After clicking the submit button or search button , flask comes here.
The values of DOI 's are obtained from the user either as string separated by comma or as a json or csv file.
Uploaded files are saved in the Upload folder.
The DOI 's are parsed and saved as a list , removed the duplicate ones.
Validated the DOI 's by checking the correct format of DOI provided by DOI.org .
The url link is obtained from doi.get_url_from_doi(doi).
Check the database for the details for each doi.
If DOI 's are not present in the database, the domains are saved as a list and Scrape object is called.
The data corresponds to the DOI 's are obtained.
:return: html page containing the bibliographical data
"""
from project_doi import database
global out_db, doi_s
list_doi = []
if request.method == 'POST':
if 'doi' in request.form:
list_doi = request.form['doi'].split(',')
if 'file' in request.files:
file = request.files['file']
if file and self.allowed_file(file.filename):
filename = secure_filename(file.filename)
extension = file.filename.rsplit('.', 1)[1].lower()
path = os.path.join(current_app.config['UPLOAD_FOLDER'],
filename)
file.save(path)
list_doi = self.upload_contents(extension, path)
else:
flash('Please upload only csv and json formats')
list_doi = list(dict.fromkeys(list_doi))
doi_s = list_doi.copy()
domain = {}
for i in list_doi:
try:
doi.validate_doi(i)
domain[i] = doi.get_real_url_from_doi(i)
except ValueError:
flash(f'{i} : is not valid , please try again')
doi_s.remove(i)
if doi_s is None:
return redirect(url_for('DOIView:index'))
doi_temp = database.check(doi_s)
if doi_temp:
doi_ = doi_temp
domains = [domain[i] for i in doi_ if i in domain]
doi_temp.clear()
scrap = scrape.Scrape()
scrap.scrape(domains, app.config['DICT_OF_SPIDERS'])
out_db = database.read(doi_s)
return render_template("search/search_doi.html", context=out_db)
def index(self):
if 'doi' in request.args:
global doi_s
doi_s = str(request.args['doi'])
else:
return 'Error:'
global out_db
if doi_s == 'all':
out_db = database.read_all()
return redirect(url_for('ApiView:display_all'))
try:
doi.validate_doi(doi_s)
domain = doi.get_real_url_from_doi(doi_s)
except ValueError:
return 'Invalid doi'
doi_temp = database.check([doi_s])
if doi_temp:
scrap = scrape.Scrape()
scrap.scrape([domain], current_app.config['DICT_OF_SPIDERS'])
out_db = database.read([doi_s])
return redirect(url_for('ApiView:display_all'))
def search_doi(self):
global out_db, doi_s
list_doi = []
if request.method == 'POST':
if 'doi' in request.form:
list_doi = request.form['doi'].split(',')
if 'file' in request.files:
file = request.files['file']
if file and self.allowed_file(file.filename):
filename = secure_filename(file.filename)
extension = file.filename.rsplit('.', 1)[1].lower()
path = os.path.join(current_app.config['UPLOAD_FOLDER'], filename)
file.save(path)
list_doi = self.upload_contents(extension, path)
else:
flash('Please upload only csv and json formats')
list_doi = list(dict.fromkeys(list_doi))
doi_s = list_doi
domain = {}
for i in list_doi:
try:
doi.validate_doi(i)
domain[i] = doi.get_real_url_from_doi(i)
except ValueError:
flash(f'{i} : is not valid , please try again')
doi_s.remove(i)
if doi_s is None:
return redirect(url_for('DOIView:index'))
doi_temp = database.check(doi_s)
if doi_temp:
doi_ = doi_temp
domains = [domain[i] for i in doi_ if i in domain]
doi_temp.clear()
scrap = scrape.Scrape()
success = scrap.scrape(domains, app.config['DICT_OF_SPIDERS'])
if success:
for i in success:
print('i in succscc', i)
out_db = database.read(doi_s)
return render_template("search/search_doi.html", context=out_db)
