def _request(self, method, mimeType, *args, **kwargs):
'dispatch to proper handler method, or return appropriate error'
try: # do we support this method?
action = getattr(self, '_' + method)
except AttributeError:
return view.report_error('%s objects do not allow %s'
% (self.name, method), 405)
try: # execute the request
o = action(*args, **kwargs)
except KeyError:
return view.report_error('Not found: %s: args=%s, kwargs=%s'
% (self.name, str(args), str(kwargs)), status=404,
webMsg="""Sorry, the data that
you requested does not exist in the database.
Please check whether you have the correct ID or spelling.""")
if isinstance(o, Response):
return o() # send the redirect
try: # do we support this mimeType?
viewFunc = getattr(self, method.lower() + '_' + mimeType)
except AttributeError:
return view.report_error('%s objects cannot return %s'
% (self.name, mimeType), 406)
try:
return viewFunc(o, **kwargs)
except Exception:
return view.report_error('view function error', 500)
def _request(self, method, mimeType, *args, **kwargs):
'dispatch to proper handler method, or return appropriate error'
try: # do we support this method?
action = getattr(self, '_' + method)
except AttributeError:
return view.report_error(
'%s objects do not allow %s' % (self.name, method), 405)
try: # execute the request
o = action(*args, **kwargs)
except KeyError:
return view.report_error('Not found: %s: args=%s, kwargs=%s' %
(self.name, str(args), str(kwargs)),
status=404,
webMsg="""Sorry, the data that
you requested does not exist in the database.
Please check whether you have the correct ID or spelling.""")
if isinstance(o, Response):
return o() # send the redirect
try: # do we support this mimeType?
viewFunc = getattr(self, method.lower() + '_' + mimeType)
except AttributeError:
return view.report_error(
'%s objects cannot return %s' % (self.name, mimeType), 406)
try:
return viewFunc(o, **kwargs)
except Exception:
return view.report_error('view function error', 500)
def default(self, docID=None, *args, **kwargs):
'process all requests for this collection'
try:
method, mimeType = request_tuple()
if docID: # a specific document from this collection
docID = IdString(docID) # implements proper cmp() vs. ObjectId
if not args: # perform the request
return self._request(method, mimeType, docID, **kwargs)
else: # pass request on to subcollection
try:
subcoll = getattr(self, args[0])
except AttributeError:
return view.report_error('no such subcollection: %s.%s'
% (self.name, args[0]), 404)
try:
parents = kwargs['parents'].copy()
except KeyError:
parents = {}
try:
parents[self.name] = self._GET(docID, parents=parents)
except KeyError:
return view.report_error('invalid ID: %s' % docID, 404,
"""Sorry, the data ID %s that
you requested does not exist in the database.
Please check whether you have the correct ID.""" % docID)
kwargs['parents'] = parents # pass dict of parents
return subcoll.default(*args[1:], **kwargs)
elif method == 'GET': # search the collection
return self._request('search', mimeType, **kwargs)
else:
return view.report_error('REST does not permit collection-%s'
% method, 405)
except Exception:
return view.report_error('REST collection error', 500)
def check_permission(self, method, personID, *args, **kwargs):
if method == 'GET': # permitted
return False
try:
if personID != get_session()['person']._id:
return view.report_error('TRAP set_interest by different user!', 403,
"You cannot change someone else's settings!")
except (KeyError,AttributeError):
return view.report_error('TRAP set_interest, not logged in!', 401,
'You must log in to access this interface')
def check_permission(self, method, *args, **kwargs):
if method == 'GET': # permitted
return False
user = get_session().get('person', None)
if not user:
return view.report_error('TRAP set_interest, not logged in!', 401,
'You must log in to access this interface')
person = kwargs['parents'].values()[0]
if person != user:
return view.report_error('TRAP set_interest by different user!', 403,
"You cannot change someone else's settings!")
def check_permission(self, method, personID, *args, **kwargs):
if method == 'GET': # permitted
return False
try:
if personID != get_session()['person']._id:
return view.report_error(
'TRAP set_interest by different user!', 403,
"You cannot change someone else's settings!")
except (KeyError, AttributeError):
return view.report_error(
'TRAP set_interest, not logged in!', 401,
'You must log in to access this interface')
def check_permission(self, method, *args, **kwargs):
if method == 'GET': # permitted
return False
user = get_session().get('person', None)
if not user:
return view.report_error(
'TRAP set_interest, not logged in!', 401,
'You must log in to access this interface')
person = kwargs['parents'].values()[0]
if person != user:
return view.report_error(
'TRAP set_interest by different user!', 403,
"You cannot change someone else's settings!")
def _search(self, searchString, searchType):
searchString = searchString.strip()
if not searchString:
s = view.report_error('empty searchString', 400,
'You did not provide a search string.')
return rest.Response(s)
# user may type "Google Search:..." into Google Search box
if searchString.lower().startswith('arxiv:'):
searchString = searchString[6:].strip()
searchType = 'arxivID'
if searchType == 'arxivID':
return rest.Redirect('/arxiv/%s' % searchString.replace('/', '_'))
elif searchType == 'arxiv':
return rest.Redirect('/arxiv?' + urlencode(dict(searchString=searchString)))
elif searchType == 'PMID':
return rest.Redirect('/pubmed/%s' % searchString)
elif searchType == 'pubmed':
return rest.Redirect('/pubmed?' + urlencode(dict(searchString=searchString)))
elif searchType == 'ncbipubmed':
return rest.Redirect('http://www.ncbi.nlm.nih.gov/sites/entrez?'
+ urlencode(dict(term=searchString,
db='pubmed')))
elif searchType == 'shortDOI':
return rest.Redirect('/shortDOI/%s' % searchString)
elif searchType == 'DOI':
dpd = core.DoiPaperData(DOI=searchString, insertNew='findOrInsert')
return rest.Redirect('/shortDOI/%s' % dpd.id)
elif searchType == 'spnetPerson':
return rest.Redirect('/people?' + urlencode(dict(searchString=searchString)))
elif searchType == 'topic':
return rest.Redirect('/topics?' + urlencode(dict(searchString=searchString)))
elif searchType == 'comment':
return rest.Redirect('/posts?' + urlencode(dict(searchAll=searchString)))
else:
raise KeyError('unknown searchType ' + searchType)
def _search(self, searchString=None, searchID=None, ipage=0,
block_size=10, session=None):
import arxiv
ipage = int(ipage)
block_size = int(block_size)
if session is None:
session = get_session()
if searchID: # just get this ID
return ParentCollection._search(self, searchID)
if not searchString:
s = view.report_error('empty searchString', 400,
'You did not provide a search string.')
return rest.Response(s)
elif arxiv.is_id_string(searchString): # just get this ID
return ParentCollection._search(self, searchString)
try: # get from existing query results
queryResults = session['queryResults']
if queryResults.get_page(ipage, self.collectionArgs['uri'],
searchString=searchString):
return queryResults
except KeyError:
pass # no stored queryResults, so construct it
pbl = view.PaperBlockLoader(arxiv.search_arxiv,
uri=self.collectionArgs['uri'])
queryResults = view.MultiplePages(pbl, block_size, ipage,
self.collectionArgs['uri'],
'arXiv.org Search Results',
searchString=searchString)
session['queryResults'] = queryResults # keep for this user
return queryResults
def _search(self, searchString=None, searchID=None, ipage=0,
block_size=20, session=None):
import pubmed
ipage = int(ipage)
block_size = int(block_size)
try: # get from existing query results
queryResults = cherrypy.session['queryResults']
if queryResults.get_page(ipage, self.collectionArgs['uri'],
searchString=searchString):
return queryResults
except KeyError:
pass # no stored queryResults, so construct it
try:
ps = pubmed.PubmedSearch(searchString, block_size)
pbl = view.PaperBlockLoader(ps, uri=self.collectionArgs['uri'])
queryResults = view.MultiplePages(pbl, block_size, ipage,
self.collectionArgs['uri'],
'Pubmed Search Results',
searchString=searchString)
except (errors.BackendFailure,KeyError):
s = view.report_error('eutils error: ' + searchString, 502,
'''Unfortunately, the NCBI eutils server
failed to perform the requested query.
To run the <A HREF="/papers?%s">same search</A> on
NCBI Pubmed, please click here. When you find a paper
of interest, you can copy its PMID (Pubmed ID) and
paste it in the search box on this page.'''
% urlencode(dict(searchType='ncbipubmed',
searchString=searchString)))
return rest.Response(s)
cherrypy.session['queryResults'] = queryResults # keep for this user
return queryResults
def _search(self, searchString, searchType):
searchString = searchString.strip()
if not searchString:
s = view.report_error('empty searchString', 400,
'You did not provide a search string.')
return rest.Response(s)
# user may type "Google Search:..." into Google Search box
if searchString.lower().startswith('arxiv:'):
searchString = searchString[6:].strip()
searchType = 'arxivID'
if searchType == 'arxivID':
return rest.Redirect('/arxiv/%s' % searchString.replace('/', '_'))
elif searchType == 'arxiv':
return rest.Redirect('/arxiv?' +
urlencode(dict(searchString=searchString)))
elif searchType == 'PMID':
return rest.Redirect('/pubmed/%s' % searchString)
elif searchType == 'pubmed':
return rest.Redirect('/pubmed?' +
urlencode(dict(searchString=searchString)))
elif searchType == 'ncbipubmed':
return rest.Redirect(
'http://www.ncbi.nlm.nih.gov/sites/entrez?' +
urlencode(dict(term=searchString, db='pubmed')))
elif searchType == 'shortDOI':
return rest.Redirect('/shortDOI/%s' % searchString)
elif searchType == 'DOI':
dpd = core.DoiPaperData(DOI=searchString, insertNew='findOrInsert')
return rest.Redirect('/shortDOI/%s' % dpd.id)
else:
raise KeyError('unknown searchType ' + searchType)
def _search(self,
searchString=None,
searchID=None,
ipage=0,
block_size=20,
session=None):
import pubmed
if not searchString:
s = view.report_error('empty searchString', 400,
'You did not provide a search string.')
return rest.Response(s)
ipage = int(ipage)
block_size = int(block_size)
try: # get from existing query results
queryResults = get_session()['queryResults']
if queryResults.get_page(ipage,
self.collectionArgs['uri'],
searchString=searchString):
return queryResults
except KeyError:
pass # no stored queryResults, so construct it
try:
ps = pubmed.PubmedSearch(searchString, block_size)
pbl = view.PaperBlockLoader(ps, uri=self.collectionArgs['uri'])
queryResults = view.MultiplePages(pbl,
block_size,
ipage,
self.collectionArgs['uri'],
'Pubmed Search Results',
searchString=searchString)
except (errors.BackendFailure, KeyError):
s = view.report_error(
'eutils error: ' + searchString, 502,
'''Unfortunately, the NCBI eutils server
failed to perform the requested query.
To run the <A HREF="/papers?%s">same search</A> on
NCBI Pubmed, please click here. When you find a paper
of interest, you can copy its PMID (Pubmed ID) and
paste it in the search box on this page.''' % urlencode(
dict(searchType='ncbipubmed', searchString=searchString)))
return rest.Response(s)
get_session()['queryResults'] = queryResults # keep for this user
return queryResults
def default(self, docID=None, *args, **kwargs):
'process all requests for this collection'
try:
method, mimeType = request_tuple()
if docID: # a specific document from this collection
docID = IdString(docID) # implements proper cmp() vs. ObjectId
invalidResponse = self.check_permission(
method, docID, *args, **kwargs)
if invalidResponse:
return invalidResponse
if not args: # perform the request
return self._request(method, mimeType, docID, **kwargs)
else: # pass request on to subcollection
try:
subcoll = getattr(self, args[0])
except AttributeError:
return view.report_error(
'no such subcollection: %s.%s' %
(self.name, args[0]), 404)
try:
parents = kwargs['parents'].copy()
except KeyError:
parents = {}
try:
parents[self.name] = self._GET(docID, parents=parents)
except KeyError:
return view.report_error(
'invalid ID: %s' % docID, 404,
"""Sorry, the data ID %s that
you requested does not exist in the database.
Please check whether you have the correct ID.""" % docID)
kwargs['parents'] = parents # pass dict of parents
return subcoll.default(*args[1:], **kwargs)
elif method == 'GET': # search the collection
return self._request('search', mimeType, **kwargs)
else:
return view.report_error(
'REST does not permit collection-%s' % method, 405)
except Exception:
return view.report_error('REST collection error', 500)
def oauth2callback(self, error=False, **kwargs):
if error:
return error
try:
oauth = get_session()['gplus_oauth']
except KeyError:
return view.report_error('session storage failed', 403,
'''Login session info storage (cookie)
failed. Please make sure that your browser accepts cookies
from selectedpapers.net. ''', traceback=False)
oauth.get_credentials(**kwargs)
get_session()['person'] = oauth.get_person()
return view.redirect('/')
def _search(self,
searchString=None,
searchID=None,
ipage=0,
block_size=10,
session=None):
import arxiv
ipage = int(ipage)
block_size = int(block_size)
if session is None:
session = get_session()
if searchID: # just get this ID
return ParentCollection._search(self, searchID)
if not searchString:
s = view.report_error('empty searchString', 400,
'You did not provide a search string.')
return rest.Response(s)
elif arxiv.is_id_string(searchString): # just get this ID
return ParentCollection._search(self, searchString)
try: # get from existing query results
queryResults = session['queryResults']
if queryResults.get_page(ipage,
self.collectionArgs['uri'],
searchString=searchString):
return queryResults
except KeyError:
pass # no stored queryResults, so construct it
pbl = view.PaperBlockLoader(arxiv.search_arxiv,
uri=self.collectionArgs['uri'])
queryResults = view.MultiplePages(pbl,
block_size,
ipage,
self.collectionArgs['uri'],
'arXiv.org Search Results',
searchString=searchString)
session['queryResults'] = queryResults # keep for this user
return queryResults
