Slow matrix download?
Closed this issue · 2 comments
kellrott commented
Need to check the performance of
c = O.query().V().where(aql.eq("_label", "Individual"))\
.where(aql.and_(aql.eq("source", "tcga"), aql.eq("disease_code", "BRCA")))\
.in_("sampleOf").mark("a").in_("expressionFor").render(["$a.name", "$.expressions"])
data = {}
for row in c:
#print("Loading:", row[0])
data[row[0]] = row[1]
samples = pandas.DataFrame(data).transpose().fillna(0.0)
kellrott commented
Based on some rough observations, it seems like a lot of the time is in the client side python code. Maybe think about trying another JSON parser ( https://artem.krylysov.com/blog/2015/09/29/benchmark-python-json-libraries/ )