def query_pubmed_for_summary_xml(unique_pmids):
history_client = EUtils.HistoryClient.HistoryClient()
pmids_dbids = EUtils.DBIds("pubmed", unique_pmids)
the_post = history_client.from_dbids(pmids_dbids)
the_esummary = the_post.esummary()
summary_xml = the_esummary.read()
return (summary_xml)
def _get_doc_summary_from_gds_ids(gds_ids):
eutils = get_eutils_client()
gds_dbids = EUtils.DBIds("gds", gds_ids)
raw_html = eutils.efetch_using_dbids(gds_dbids,
rettype="docsum",
retmode="html").read()
return (raw_html)
def computeE(self, periodic=True):
for i in range(self.N):
atomi = self.atoms[i]
if periodic:
E = EUtils.computeEPeriodic(self.source, atomi, self.cr,
self.lmbdax, self.lmbday)
else:
E = EUtils.computeE(self.source, atomi)
atomi.ex = E[0]
atomi.ey = E[1]
atomi.ez = E[2]
return
def pmcids_to_pmids(pmcids):
if not pmcids:
return []
entrez = HistoryClient.HistoryClient(eutils=get_eutils_client())
pmcids_dbids = EUtils.DBIds("pmc", pmcids)
pmcids_records = entrez.post(pmcids_dbids)
pmc_link_query = pmcids_records.elink(db="pubmed")
raw_xml = pmc_link_query.read()
pmids = _extract_pmid_links_from_xml(raw_xml)
return (pmids)
def get_a_FakeHistoryClient_miss():
import EUtils
FakeHistoryClient_miss = fudge.Fake('FakeHistoryClient_miss')
FakeHistoryClient_miss = FakeHistoryClient_miss.provides("__init__")
FakeHistoryClient_miss = FakeHistoryClient_miss.expects("post").returns(
fudge.Fake("post_return", allows_any_call=True))
fake_search_return = fudge.Fake("search_return").has_attr(
dbids=EUtils.DBIds("pubmed", test_data_geo_filtered_pmids))
FakeHistoryClient_miss = FakeHistoryClient_miss.expects("search").returns(
fake_search_return)
return (FakeHistoryClient_miss)
def fetch_articles(article_ids):
print "fetching abstracts..."
print article_ids
#handle = Entrez.efetch(db="pubmed",id=article_ids,rettype="medline",retmode="text")
dbids = EUtils.DBIds("pubmed", [str(xid) for xid in article_ids])
client = ThinClient.ThinClient()
# fix for new NCBI API
handle = client.efetch_using_dbids(dbids=dbids,
rettype='medline',
retmode='text')
#handle = EUtils.efetch(db="pubmed",id=article_ids,rettype="medline",retmode="text")
records = Medline.parse(handle)
print "Done."
return records
def filter_pmcids(query_pmcids, filter_string):
if VERBOSE:
print "filter %s" % filter_string
if not query_pmcids:
return ([])
try:
time.sleep(1 / 3)
entrez = HistoryClient.HistoryClient(eutils=get_eutils_client())
pmcids_dbids = EUtils.DBIds("pmc", query_pmcids)
pmcids_records = entrez.post(pmcids_dbids)
filtered_pmcid_records = entrez.search(
'#%s AND %s' % (pmcids_records.query_key, filter_string), db="pmc")
filtered_pmcids = filtered_pmcid_records.dbids.ids
except AttributeError:
filtered_pmcids = []
except EUtils.EUtilsError, e:
if e.args[0].strip() == "Empty result - nothing todo":
filtered_pmcids = []
else:
raise datasourcesError(e)
def solve(): x = np.int64(600851475143) ps = eu.primes(int(np.sqrt(x))) return np.max([p for p in ps if x % p == 0])
def solve(): p = eu.primes(200000) return p[10001 - 1]
def _get_gds_links_from_pmid(pmid):
eutils = get_eutils_client()
pmids_dbids = EUtils.DBIds("pubmed", pmid)
xml = eutils.elink_using_dbids(pmids_dbids, db="gds").read()
return (xml)
def get_history_client_post(pmids):
history_client = get_eutils_history_client()
pmids_dbids = EUtils.DBIds("pubmed", pmids)
the_post = history_client.post(pmids_dbids)
return (history_client, the_post)
def solve(): fibs = eu.to_array(fib(4000000), int) return np.sum(np.select([fibs % 2 == 0], [fibs]))
