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extract author/org/paper from aminer json data toimport neo4j
#!/usr/bin/env python
# encoding: utf-8
import json
import os
import sys
import uuid
import traceback
from concurrent import futures
num_workers = 12
folder = '/mnt/lun2/docker_image/neo4j-aminer/out'
if not os.path.exists(folder):
os.makedirs(folder)
def extract_author_paper(filename):
prefix = folder + '/' + filename.split('_')[-1][:-4] + '_'
orgs = []
authors = []
p_a = []
a_o = []
cite_rel = []
all_paper = []
paper_info = {}
paper_id = []
name_id = {}
org_id = {}
for i, node in enumerate(open(filename)):
node = json.loads(node)
if 'id' not in node:
continue
if "authors" in node:
for a in node['authors']:
if 'name' not in a or not a['name']:
continue
name = a['name'][:500].replace(',', ' ')
if name not in name_id:
nameId = str(uuid.uuid5(uuid.NAMESPACE_DNS, name.encode('utf-8')))
name_id[name] = nameId
nameId = name_id[name]
if 'org' in a and a['org']:
org = a['org'][:500].replace(",", ' ')
if org not in org_id:
orgId = str(uuid.uuid5(uuid.NAMESPACE_OID, org.encode('utf-8')))
org_id[org] = orgId
orgId = org_id[org]
orgs.append(','.join([orgId, org, 'Org']))
a_o.append(','.join((nameId, orgId, 'WORK_IN')))
p_a.append(','.join([nameId, node['id'], 'WRITE']))
authors.append(','.join([nameId, name, 'Author']))
pid = node['id']
title = node.get('title', '').replace('\n', '').replace(',', ' ')
year = node.get('year', '')
publisher = node.get('publisher', '').replace(',', ' ')
venue = node.get('venue', '').replace(',', ' ')
keywords = ';'.join(node.get('keywords', [])).replace(',', ' ')
fos = ';'.join(node.get('fos', [])).replace(',', ' ')
n_citation = str(node.get('n_citation', 0)).replace(',', ' ')
page_start = node.get('page_start', '').replace(',', ' ')
page_end = node.get('page_end', '').replace(',', ' ')
doc_type = node.get('doc_type', '').replace(',', ' ')
lang = node.get('lang', '').replace(',', ' ')
volume = node.get('volume', '').replace(',', ' ')
issue = node.get('issue', '').replace(',', ' ')
issn = node.get('issn', '').replace(',', ' ')
isbn = node.get('isbn', '').replace(',', ' ')
doi = node.get('doi', '').replace(',', ' ')
pdf = node.get('pdf', '').replace(',', ' ')
url = ';'.join(node.get('url', [])).replace(',', ' ')
node_info = [pid, title, str(year), publisher, venue, keywords, fos, n_citation, page_start, page_end,
doc_type, lang, volume, issue, issn, isbn, doi, pdf, url, 'Paper']
all_paper.append(','.join(node_info))
paper_id.append(pid) # [pid] = node_info
# paper_info[pid] = ','.join(node_info)
if "references" in node:
for j in node['references']:
cite_rel.append(','.join([node['id'], j, 'REFERENCE']))
# paper_id.append(j)
if i % 500000 == 0:
print("the {} txt: {} lines finished".format(prefix[:-1], i))
all_paper = list(set(all_paper))
orgs = list(set(orgs))
a_o = list(set(a_o))
p_a = list(set(p_a))
authors = list(set(authors))
a_p_out = open(prefix + "paper_author.csv", 'w')
a_out = open(prefix + "author.csv", 'w')
o_out = open(prefix + "org.csv", 'w')
a_o_out = open(prefix + "author_org.csv", 'w')
rel_file = open(prefix + "cite_relation.csv", 'w')
node_file = open(prefix + "paper.csv", 'w')
a_p_out.write(":START_ID,:END_ID,:TYPE\n")
a_o_out.write(":START_ID,:END_ID,:TYPE\n")
rel_file.write(':START_ID,:END_ID,:TYPE\n')
node_file.write('paperId:ID,title,year,publisher,venue,keywords,fos,n_citation,page_start,page_end,doc_type,lang,volume,issue,issn,isbn,doi,pdf,url,:LABEL\n')
a_out.write("authorId:ID,name,:LABEL\n")
o_out.write("orgId:ID,name,:LABEL\n")
o_out.write('\n'.join(orgs).replace("'", '').replace('"', '').encode("utf-8"))
o_out.close()
del orgs
a_o_out.write('\n'.join(a_o).replace("'", '').replace('"', '').encode("utf-8"))
a_o_out.close()
del a_o
a_p_out.write("\n".join(p_a).replace("'", '').replace('"', '').encode("utf-8"))
a_p_out.close()
del p_a
a_out.write("\n".join(authors).replace("'", '').replace('"', '').encode("utf-8"))
a_out.close()
del authors
node_file.write("\n".join(all_paper).replace("'", '').replace('"', '').encode("utf-8"))
node_file.close()
del all_paper
rel_file.write('\n'.join(cite_rel).encode('utf-8'))
rel_file.close()
del cite_rel
def main():
source = '/mnt/lun2/aminer/www.aminer.cn/aminer_papers'
all_file = [os.path.join(source, i) for i in os.listdir(source)]
with futures.ProcessPoolExecutor(num_workers) as executor:
f_tasks = {executor.submit(extract_author_paper, filename): filename for filename in all_file}
for f in f_tasks:
if f.running():
print("{} is running".format(f))
for f in futures.as_completed(f_tasks):
fn = f_tasks[f]
try:
f.result()
print("{} has finished.".format(fn[44:]))
except Exception as e:
print traceback.format_exc()
print("{} has an exception: {}".format(fn[44:], e))
if __name__ == '__main__':
main()
# extract_author_paper('/data/aminer_papers/aminer_papers_10.txt')
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