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create-aliases.py
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create-aliases.py
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import os
import yaml
import json
import py2neo
import pandas
import pymongo
import logging
import requests
import datetime
import argparse
import lxml.html
from sys import exit
from pprint import pprint
from urllib.parse import quote
class CreateAlias():
def __init__(self,config):
logging.basicConfig(
level=logging.INFO,
filename= 'pipeline.log',
datefmt='%Y-%m-%d %H:%M:%S',
format='%(asctime)s %(levelname)-8s %(message)s')
self.logger = logging.getLogger('pipeline')
name_yml = os.path.abspath(config)
with open(name_yml, 'r') as ymlfile:
cfg = yaml.load(ymlfile,Loader=yaml.BaseLoader)
client = pymongo.MongoClient('mongodb://{0}:{1}@{2}/{3}'.format(
quote(cfg['auth'][cfg['env']]['mongo-user']),
quote(cfg['auth'][cfg['env']]['mongo-pass']),
cfg['auth'][cfg['env']]['mongo-host'],
cfg['auth'][cfg['env']]['mongo-db'])
)
self.graph = py2neo.Graph(
password = cfg['auth'][cfg['env']]['neo4j-pass'],
host = cfg['auth'][cfg['env']]['neo4j-host']
)
self.db = client[cfg['auth'][cfg['env']]['mongo-db']]
self.bfi_and_oai = 'BFI_andOAI'
self.alias_org_name_hospital = 'alias_org_name_hospital'
self.alias_org_type = 'alias_org_type'
self.alias_topic_type = 'alias_topic_type'
self.alias_uni_org_type = 'alias_uni_org_type'
self.graph.run(f'CREATE INDEX ON:Document(doi);')
self.graph.run(f'CREATE INDEX ON:Organisation(id_original);')
self.graph.run(f'CREATE INDEX ON:Organisation(types);')
self.graph.run(f'CREATE INDEX ON:Topic(title);')
self.graph.run(f'CREATE INDEX ON:Organisation(name);')
def process(self):
bfi_and_oai = self.db[self.bfi_and_oai].find({},{'_id' : 0})
alias_org_name_hospital = self.db[self.alias_org_name_hospital].find({},{'_id' : 0})
alias_org_type = self.db[self.alias_org_type].find({},{'_id' : 0})
alias_topic_type = self.db[self.alias_topic_type].find({},{'_id' : 0})
alias_uni_org_type = self.db[self.alias_uni_org_type].find({},{'_id' : 0})
pandas.DataFrame(bfi_and_oai).to_csv(f'/var/lib/neo4j/import/bfi_and_oai.csv',encoding='utf-8',index=False,sep='|')
pandas.DataFrame(alias_org_name_hospital).to_csv(f'/var/lib/neo4j/import/alias_org_name_hospital.csv',encoding='utf-8',index=False,sep='|')
pandas.DataFrame(alias_org_type).to_csv(f'/var/lib/neo4j/import/alias_org_type.csv',encoding='utf-8',index=False,sep='|')
pandas.DataFrame(alias_topic_type).to_csv(f'/var/lib/neo4j/import/alias_topic_type.csv',encoding='utf-8',index=False,sep='|')
pandas.DataFrame(alias_uni_org_type).to_csv(f'/var/lib/neo4j/import/alias_uni_org_type.csv',encoding='utf-8',index=False,sep='|')
cypher = """
LOAD CSV WITH HEADERS FROM 'file:///bfi_and_oai.csv' AS row FIELDTERMINATOR '|'
MATCH( d:Document{ doi:row.DOI })
SET
d.bfiandoai_type = row.`Type`,
d.bfiandoai_oai_pub_year = row.`OAI-pub-year`,
d.bfiandoai_oai_mra = row.`OAI-MRA`,
d.bfiandoai_oai_sub_year = row.`OAI-sub-year`,
d.bfiandoai_bfi_level = row.`BFI-Level`,
d.bfiandoai_oai_class = row.`OAI-Class`,
d.bfiandoai_bfi_mra = row.`BFI-MRA`,
d.bfiandoai_bfi_pub_year = row.`BFI-pub-year`,
d.bfiandoai_bfi_sub_year = row.`BFI-sub-year`
"""
properties_set = self.graph.run(cypher).stats().properties_set
self.logger.info(f' BFI_andOAI {properties_set}')
cypher = """
LOAD CSV WITH HEADERS FROM 'file:///alias_org_name_hospital.csv' AS row FIELDTERMINATOR '|'
MATCH (o:Organisation { id_original : row.GRID})
SET o.alias_org_name_hospital = row.ALIAS
"""
properties_set = self.graph.run(cypher).stats().properties_set
self.logger.info(f' alias_org_name_hospital {properties_set}')
cypher = """
LOAD CSV WITH HEADERS FROM 'file:///alias_org_type.csv' AS row FIELDTERMINATOR '|'
MATCH (o:Organisation { types : row.PREVIOUS})
SET o.alias_org_type = row.NEW
"""
properties_set = self.graph.run(cypher).stats().properties_set
self.logger.info(f' alias_org_type {properties_set}')
cypher = """
LOAD CSV WITH HEADERS FROM "file:///alias_topic_type.csv" AS row FIELDTERMINATOR '|'
MATCH (t:Topic { title : row.PREVIOUS})
SET t.alias_topic_type = row.NEW
"""
properties_set = self.graph.run(cypher).stats().properties_set
self.logger.info(f' alias_topic_type {properties_set}')
cypher = """
LOAD CSV WITH HEADERS FROM "file:///alias_uni_org_type.csv" AS row FIELDTERMINATOR '|'
MATCH (o:Organisation { name : row.PREVIOUS})
SET o.alias_uni_org_type = row.NEW
"""
properties_set = self.graph.run(cypher).stats().properties_set
self.logger.info(f' alias_uni_org_type {properties_set}')
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-cfg','--config',default='./config.yml')
args = parser.parse_args()
config = args.config
CreateAlias(config).process()