def test_fetch_ids(self):
"""This also tests 'SAXmed.eFetchResultHandler'."""
(abs1, abs2) = eUtils.fetch_ids(['22180407', '23580981'])
target_title1 = u'Update on PARP1 inhibitors in ovarian cancer.'
target_title2 = u'Replication clamps and clamp loaders.'
self.assertEqual(abs1['title'], target_title1)
self.assertEqual(abs2['title'], target_title2)
def post(self):
# Who is it? Get it from the POST parameters.
uid = self.request.get('uid')
data = models.UserData.get_by_key_name(uid)
# Check that POST is issued from PubCron mail.
checksum = self.validate_request(data)
if not self.request.get('checksum'):
# Could not check identity (hacked?!!): good-bye.
return
# Identity check successful. Do the update.
new_relevant_pmids = []
new_irrelevant_pmids = []
# Process key/value pairs.
for name in self.request.arguments():
# NB: only PMID update correspond to 'name' equal to
# "Yes" or "No". The other cases are either no answer
# or non PMID POST paramters (like uid or checksum).
if self.request.get(name) == 'Yes':
new_relevant_pmids += [name]
elif self.request.get(name) == 'No':
new_irrelevant_pmids += [name]
# It is unlikely that a malicious request went
# until here, but because we are about to save user-
# submitted data, we do a validity (security) check.
pmids_to_update = new_relevant_pmids + new_irrelevant_pmids
if not self.validate_pmid(pmids_to_update):
# Validation failed: good-bye.
return
# From here, PMIDs have been parsed and checked.
# Now recall and parse user JSON data.
mu_corpus = utils.decrypt(data, 'mu_corpus')
relevant_docs = utils.decrypt(data, 'relevant_docs')
irrelevant_docs = utils.decrypt(data, 'irrelevant_docs')
# Clear new docs from user data (in case users are notifying
# that they change their mind on relevance).
pmids_to_update = new_relevant_pmids + new_irrelevant_pmids
for relevant_then_irrelevant in (relevant_docs, irrelevant_docs):
for doc in relevant_then_irrelevant:
if doc.get('pmid') in pmids_to_update:
relevant_then_irrelevant.remove(doc)
# Now, get the PubMed data and compute tf-idf.
for (new_ids, doc_list) in (
(new_relevant_pmids, relevant_docs),
(new_irrelevant_pmids, irrelevant_docs)):
new_docs = eUtils.fetch_ids(new_ids)
new_tfidf = tfidf.compute_from_texts(
[abstr.get('text', '') for abstr in new_docs],
mu_corpus.values()
)
for (doc, tfidf_dict) in zip (new_docs, new_tfidf):
# Keep only fields 'pmid' and 'title'.
for field_name in doc.keys():
if not field_name in ('pmid', 'title'):
doc.pop(field_name, None)
# Add field 'tfidf'.
doc['tfidf'] = tfidf_dict
# Append to user data.
doc_list.extend(new_docs)
and_finally_remove_junk_from(doc_list)
# Update the documents...
data.relevant_docs = zlib.compress(json.dumps(relevant_docs))
data.irrelevant_docs = zlib.compress(json.dumps(irrelevant_docs))
# ... and put.
data.put()
# Now reassure the user.
self.response.out.write(utils.render('feedback.html'))
