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Faster neo4j drug, synonym and drug insertion #64

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Merged
bechbd merged 16 commits into from
Apr 17, 2020
Merged

Faster neo4j drug, synonym and drug insertion #64

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e1251c1
neo4j speedup skeleton
007vasy Apr 16, 2020
78029e9
async scrape speedup
007vasy Apr 17, 2020
e6bb658
async scrape speedup
007vasy Apr 17, 2020
73546bc
neo4j speedup skeleton
007vasy Apr 16, 2020
effa6cd
async scrape speedup
007vasy Apr 17, 2020
6a02d0d
async scrape speedup
007vasy Apr 17, 2020
bd49c68
rebase
007vasy Apr 17, 2020
a7414f7
async study and drug scraping for speedup
007vasy Apr 17, 2020
861822e
unwind for drugs
007vasy Apr 17, 2020
7b070b8
file cleanup
007vasy Apr 17, 2020
f1436cc
added loading bar
007vasy Apr 17, 2020
79eb5e3
added loading bar
007vasy Apr 17, 2020
a98e666
batch node and edge merging for drugs and synonyms
007vasy Apr 17, 2020
ab69560
batch node and edge merging for drugs and synonyms
007vasy Apr 17, 2020
c568845
batch edge tested
007vasy Apr 17, 2020
5ba15db
all merged batched
007vasy Apr 17, 2020
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async scrape speedup
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@007vasy
007vasy committed Apr 17, 2020
commit e6bb6587af7aa66d3c6bc14e14c7dc6ce55be7de
13 changes: 13 additions & 0 deletions IngestDrugSynonymsWF.py
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from modules.IngestDrugSynonyms import IngestDrugSynonyms
from modules.DrugSynonymDataToNeo4j import DrugSynonymDataToNeo4j
import logging

logging.basicConfig(format='>>> %(message)s', level=logging.INFO)

drugSynonym = IngestDrugSynonyms()
drugSynonym.auto_get_and_clean_data()

neo4jBridge = DrugSynonymDataToNeo4j()
neo4jBridge.upload_drugs_and_synonyms(drugSynonym.drug_vocab)
neo4jBridge.upload_studies(drugSynonym.all_studies_df)