def rrid_wrapper(request, username, api_token, group, logloc):
""" Receive an article, parse RRIDs, resolve them, create annotations, log results """
if request.method == 'OPTIONS':
response = Response()
request_headers = request.headers['Access-Control-Request-Headers'].lower()
request_headers = re.findall('\w(?:[-\w]*\w)', request_headers)
response_headers = ['access-control-allow-origin']
for req_acoa_header in request_headers:
if req_acoa_header not in response_headers:
response_headers.append(req_acoa_header)
response_headers = ','.join(response_headers)
response.headers.update({
'Access-Control-Allow-Origin': '*',
'Access-Control-Allow-Headers': '%s' % response_headers
})
response.status_int = 204
return response
h = HypothesisUtils(username=username, token=api_token, group=group)
target_uri = urlparse.parse_qs(request.text)['uri'][0]
params = { 'limit':200, 'uri':target_uri }
query_url = h.query_url_template.format(query=urlencode(params, True))
obj = h.authenticated_api_query(query_url)
rows = obj['rows']
tags = set()
for row in rows:
if row['group'] != h.group: # api query returns unwanted groups
continue
elif row['user'] != 'acct:' + h.username + '@hypothes.is':
continue
for tag in row['tags']:
if tag.startswith('RRID'):
tags.add(tag)
html = urlparse.parse_qs(request.text)['data'][0]
print(target_uri)
found_rrids = {}
try:
matches = re.findall('(.{0,10})(RRID(:|\)*,*)[ \t]*)(\w+[_\-:]+[\w\-]+)([^\w].{0,10})', html.replace('–','-'))
existing = []
for match in matches:
print(match)
prefix = match[0]
exact = match[3]
if 'RRID:'+exact in tags:
print('skipping %s, already annotated' % exact)
continue
new_tags = []
if exact in existing:
new_tags.append('RRIDCUR:Duplicate')
else:
existing.append(exact)
found_rrids[exact] = None
suffix = match[4]
print('\t' + exact)
resolver_uri = 'https://scicrunch.org/resolver/%s.xml' % exact
r = requests.get(resolver_uri)
print(r.status_code)
xml = r.content
found_rrids[exact] = r.status_code
if r.status_code < 300:
root = etree.fromstring(xml)
if root.findall('error'):
s = 'Resolver lookup failed.'
s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
r = h.create_annotation_with_target_using_only_text_quote(url=target_uri, prefix=prefix, exact=exact, suffix=suffix, text=s, tags=new_tags + ['RRIDCUR:Unresolved'])
print('ERROR')
else:
data_elements = root.findall('data')[0]
s = ''
data_elements = [(e.find('name').text, e.find('value').text) for e in data_elements] # these shouldn't duplicate
citation = [(n, v) for n, v in data_elements if n == 'Proper Citation']
name = [(n, v) for n, v in data_elements if n == 'Name']
data_elements = citation + name + sorted([(n, v) for n, v in data_elements if (n != 'Proper Citation' or n != 'Name') and v is not None])
for name, value in data_elements:
if (name == 'Reference' or name == 'Mentioned In Literature') and value is not None and value.startswith('<a class'):
if len(value) > 500:
continue # nif-0000-30467 fix keep those pubmed links short!
s += '<p>%s: %s</p>' % (name, value)
s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
r = h.create_annotation_with_target_using_only_text_quote(url=target_uri, prefix=prefix, exact=exact, suffix=suffix, text=s, tags=new_tags + ['RRID:'+exact])
else:
s = 'Resolver lookup failed.'
r = h.create_annotation_with_target_using_only_text_quote(url=target_uri, prefix=prefix, exact=exact, suffix=suffix, text=s, tags=new_tags + ['RRIDCUR:Unresolved'])
except:
print(traceback.print_exc())
results = ', '.join(found_rrids.keys())
r = Response(results)
r.content_type = 'text/plain'
r.headers.update({
'Access-Control-Allow-Origin': '*'
})
try:
now = datetime.now().isoformat()[0:19].replace(':','').replace('-','')
fname = logloc + 'rrid-%s.log' % now
s = 'URL: %s\n\nResults: %s\n\nCount: %s\n\nText:\n\n%s' % ( target_uri, results, len(found_rrids), html )
with open(fname, 'wb') as f:
f.write(s.encode('utf-8'))
except:
print(traceback.print_exc())
return r
def rrid(request):
""" Receive an article, parse RRIDs, resolve them, create annotations, log results """
if request.method == 'OPTIONS':
response = Response()
request_headers = request.headers[
'Access-Control-Request-Headers'].lower()
request_headers = re.findall('\w(?:[-\w]*\w)', request_headers)
response_headers = ['access-control-allow-origin']
for req_acoa_header in request_headers:
if req_acoa_header not in response_headers:
response_headers.append(req_acoa_header)
response_headers = ','.join(response_headers)
response.headers.update({
'Access-Control-Allow-Origin':
'*',
'Access-Control-Allow-Headers':
'%s' % response_headers
})
response.status_int = 204
return response
h = HypothesisUtils(username=username, token=api_token, group=group)
target_uri = urlparse.parse_qs(request.text)['uri'][0]
params = {'limit': 200, 'uri': target_uri}
query_url = h.query_url_template.format(query=urlencode(params, True))
obj = h.authenticated_api_query(query_url)
rows = obj['rows']
tags = set()
for row in rows:
if row['group'] != h.group: # api query returns unwanted groups
continue
elif row['user'] != 'acct:' + h.username + '@hypothes.is':
continue
for tag in row['tags']:
if tag.startswith('RRID'):
tags.add(tag)
html = urlparse.parse_qs(request.text)['data'][0]
print(target_uri)
found_rrids = {}
try:
matches = re.findall('(.{0,10})(RRID:\s*)([_\w\-:]+)([^\w].{0,10})',
html.replace('–', '-'))
existing = []
for match in matches:
print(match)
prefix = match[0]
exact = match[2]
if 'RRID:' + exact in tags:
print('skipping %s, already annotated' % exact)
continue
new_tags = []
if exact in existing:
new_tags.append('RRIDCUR:Duplicate')
else:
existing.append(exact)
found_rrids[exact] = None
suffix = match[3]
print('\t' + exact)
resolver_uri = 'https://scicrunch.org/resolver/%s.xml' % exact
r = requests.get(resolver_uri)
print(r.status_code)
xml = r.content
found_rrids[exact] = r.status_code
if r.status_code < 300:
root = etree.fromstring(xml)
if root.findall('error'):
s = 'Resolver lookup failed.'
s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
r = h.create_annotation_with_target_using_only_text_quote(
url=target_uri,
prefix=prefix,
exact=exact,
suffix=suffix,
text=s,
tags=new_tags + ['RRIDCUR:Unresolved'])
print('ERROR')
else:
data_elements = root.findall('data')[0]
s = ''
data_elements = [
(e.find('name').text, e.find('value').text)
for e in data_elements
] # these shouldn't duplicate
citation = [(n, v) for n, v in data_elements
if n == 'Proper Citation']
name = [(n, v) for n, v in data_elements if n == 'Name']
data_elements = citation + name + sorted(
[(n, v) for n, v in data_elements
if (n != 'Proper Citation' or n != 'Name')
and v is not None])
for name, value in data_elements:
if (name == 'Reference'
or name == 'Mentioned In Literature'
) and value is not None and value.startswith(
'<a class'):
if len(value) > 500:
continue # nif-0000-30467 fix keep those pubmed links short!
s += '<p>%s: %s</p>' % (name, value)
s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
r = h.create_annotation_with_target_using_only_text_quote(
url=target_uri,
prefix=prefix,
exact=exact,
suffix=suffix,
text=s,
tags=new_tags + ['RRID:' + exact])
else:
s = 'Resolver lookup failed.'
r = h.create_annotation_with_target_using_only_text_quote(
url=target_uri,
prefix=prefix,
exact=exact,
suffix=suffix,
text=s,
tags=new_tags + ['RRIDCUR:Unresolved'])
except:
print(traceback.print_exc())
results = ', '.join(found_rrids.keys())
r = Response(results)
r.content_type = 'text/plain'
r.headers.update({'Access-Control-Allow-Origin': '*'})
try:
now = datetime.now().isoformat()[0:19].replace(':',
'').replace('-', '')
fname = 'rrid-%s.log' % now
s = 'URL: %s\n\nResults: %s\n\nCount: %s\n\nText:\n\n%s' % (
target_uri, results, len(found_rrids), html)
with open(fname, 'wb') as f:
f.write(s.encode('utf-8'))
except:
print(traceback.print_exc())
return r
