def searchByTerms(terms, minresults=10, earlyyear=0, lateyear=3000):
sortedterms = mb.sortImportance(terms)
nr_of_results = 0
while ((nr_of_results < minresults) and (len(sortedterms) > 0)):
query = querybuilder.buildQuery(sortedterms, [], 4, earlyyear, lateyear)
resp, content = h.request(baseURL + \
"esearch.fcgi?db=pubmed&retmode=xml&sort=relevance" + \
"&retmax=" + str(retmax) + "&term=" + \
query.replace(" ", "+"))
resultsdict = xmltodict.parse(content)["eSearchResult"]
nr_of_results = int(resultsdict["Count"])
print "Number of results for %i terms: %i" \
% (len(sortedterms), nr_of_results)
sortedterms.pop()
return query, resultsdict, nr_of_results
def searchByCombination(primaryterms, secondaryterms, minresults=10,
earlyyear=0, lateyear=3000):
level = 4
nr_of_results = -1
while ((nr_of_results < minresults) and (level > 0)):
query = querybuilder.buildQuery(primaryterms, secondaryterms, level, \
earlyyear, lateyear)
#print query
resp, content = h.request(baseURL + \
"esearch.fcgi?db=pubmed&retmode=xml&sort=relevance&" + \
"retmax=" + str(retmax) + "&term=" + query.replace(" ", "+"))
resultsdict = xmltodict.parse(content)["eSearchResult"]
try:
nr_of_results = int(resultsdict["Count"])
except KeyError:
print "KeyError"
nr_of_results = 0
print "Number of results for level %i: %i" \
% (level, nr_of_results)
level -= 1
return query, resultsdict, nr_of_results
secondaryterms = []
if len(evidence) == 1:
for term in terms:
if terms[term]["major"] >= 1:
primaryterms.append(("(\"" + term + "\"[MeSH Terms] OR \"" + term + "\"[All Fields])"))
else:
subquery = ""
for term in terms:
# make conjunction of all terms that occur in all articles
if terms[term]["count"] > (len(evidence) - 1):
primaryterms.append(("(\"" + term + "\"[MeSH Terms] OR \"" + term + "\"[All Fields])"))
# all rank 2 terms
if terms[term]["count"] == (len(evidence) - 1):
secondaryterms.append(("\"" + term + "\"[MeSH Terms]"))
query2 = querybuilder.buildQuery(primaryterms, secondaryterms, 1)
# write to results.html
out.write("<h3>Query obtained from input article MeSH terms</h3>")
out.write(query2)
#--------------------------------------
# PART 3: execute (combined) query)
#--------------------------------------
# combine with old query
#query += (" AND \"" + query2)
# add dates
#query += " 2004:2012 [mhda]"
