def add_coauthor_relation(begin,end,msg):
'''
coauthor times and coauthor relationships
:return:
mag_authors0411:
{coauthor_counts:n}
{coauthor_list:[{year:1999,id:1000000},year:1998,id:1000001}]}
'''
start_time = time()
print(start_time)
col1 = connectTable("qiuzh", "mag_papers0415")
col2 = connectTable("qiuzh", "mag_authors0411")
operation = []
cursor = col2.find(no_cursor_timeout=True)[begin:end]
for i in cursor:
author_id = i["_id"]
coauthor_times = 0
coauthor_list = []
papers = i["new_pubs"]
for paper in papers:
paper_details = col1.find_one({"_id": paper})
# if paper_details:
coauthor_times += (len(paper_details["authors"]) - 1)
for author in paper_details["authors"]:
if author["id"] != author_id:
coauthor_list.append({"coauthor_id": author["id"], "coauthor_time": paper_details["year"]})
if len(coauthor_list)>0:
operation.append(pymongo.UpdateOne({"_id": author_id},
{"$set": {"coauthor_counts": coauthor_times, "coauthor": coauthor_list}}))
print(msg,"线程已完成",len(operation),flush=True)
col2.bulk_write(operation, ordered=False)
cursor.close()
print(msg,time(), (time() - start_time))
def author_citation_number(begin, end, msg):
'''
this function is appropriate for mag_authors0510 and citation network0515
:return:
'''
colpaper = connectTable("qiuzh", "mag_papers0510")
col_author = connectTable("qiuzh", "mag_authors0510")
count = 0
operation = []
cursor = col_author.find(no_cursor_timeout=True)[begin:end]
for author in cursor:
count += 1
author_id = author["_id"]
citation_number = 0
for paper in author["new_pubs"]:
p = colpaper.find_one({"_id": paper["pid"]},
no_cursor_timeout=True)
citation_number += p["cn"]
operation.append(
pymongo.UpdateOne({"_id": author_id},
{"$set": {
"cn": citation_number
}}))
if count % 10000 == 0:
print(msg, "已处理:", count / 10000, flush=True)
col_author.bulk_write(operation, ordered=False)
print(msg, "已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col_author.bulk_write(operation, ordered=False)
cursor.close()
def clone_collection():
coll = connectTable("oga_one", "mag_paper_plus2")
# col2 = connectTable("qiuzh","MAG_authors")
col3 = connectTable("qiuzh", "papers")
for i in coll.find({"$and": [{"venue": {"$exists": True}}]}):
col3.insert_one(i)
print(col3.find().count())
def divide_researchers_into_2groups():
col_author = connectTable("qiuzh", "mag_researchers0810")
col1 = connectTable("qiuzh", "researchers0810_trainingset")
col2 = connectTable('qiuzh', "researchers0810_testset")
opt1 = []
opt2 = []
count = 0
cursor = col_author.find(no_cursor_timeout=True)
for researcher in col_author.find():
count += 1
if researcher["first_year"] <= 1996:
opt1.append(pymongo.InsertOne(researcher))
else:
opt2.append(pymongo.InsertOne(researcher))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col1.bulk_write(opt1, ordered=False)
print("已写入:", len(opt1), flush=True)
col2.bulk_write(opt2, ordered=False)
print("已写入:", len(opt2), flush=True)
opt1 = []
opt2 = []
if opt1:
col1.bulk_write(opt1, ordered=False)
print("又写入:", len(opt1), flush=True)
if opt2:
col2.bulk_write(opt2, ordered=False)
print("又写入:", len(opt2), flush=True)
cursor.close()
def match_v1_v2_id(begin, end, msg):
coll = connectTable("qiuzh", "mag_papers")
coll3 = connectTable('qiuzh', "mag_authors0409")
opt = []
count = 0
cursor = coll3.find(no_cursor_timeout=True)[begin:end]
for i in cursor:
if count % 100000 == 0:
print("线程： %s, 已完成 %s 万条" % (msg, count / 100000), flush=True)
count += 1
v2author_id = i.get("_id")
# print(v2author_id)
new_pubs = []
papers = coll.find({"authors.id": v2author_id})
for paper in papers:
id = paper.get("_id")
new_pubs.append(id)
opt.append(
pymongo.UpdateOne({"_id": v2author_id},
{"$set": {
"new_pubs": new_pubs
}}))
cursor.close()
coll3.bulk_write(opt, ordered=False)
print("线程： %s, 遍历了 %s" % (msg, len(opt)))
def researchers_con():
'''
the coauthor times based on the mag_authors0510
:return:
'''
col1 = connectTable('qiuzh', "mag_authors0510")
col2 = connectTable('qiuzh', "mag_researchers0707")
count = 0
operation = []
cursor = col2.find(no_cursor_timeout=True)
for author in cursor:
count += 1
author_id = author["_id"]
coauthor_number = col1.find_one({"_id": author_id})["con"]
operation.append(
pymongo.UpdateOne({"_id": author_id},
{"$set": {
"con": coauthor_number
}}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col2.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
if operation:
col2.bulk_write(operation, ordered=False)
print("又处理", len(operation))
cursor.close()
def paper_citation_number(begin, end, msg):
'''
this function is appropriate for citation_network0515 and mag_papers0510
:return: add each papers' total citation in mag_papers0510
'''
colpaper = connectTable("qiuzh", "mag_papers0510")
col_citation_network = connectTable("qiuzh",
"citation_network0810_trainingset")
count = 0
operation = []
cursor = colpaper.find(no_cursor_timeout=True)[begin:end]
for paper in cursor:
count += 1
paper_id = paper["_id"]
citation_number = 0
paper_citation_relations = col_citation_network.find(
{"id": paper_id}, no_cursor_timeout=True)
if paper_citation_relations:
for paper_citation_relation in paper_citation_relations:
citation_number += len(paper_citation_relation["citation"])
operation.append(
pymongo.UpdateOne({"_id": paper_id},
{"$set": {
"cn_before1996": citation_number
}}))
if count % 10000 == 0:
print(msg, "已处理:", count / 10000, flush=True)
colpaper.bulk_write(operation, ordered=False)
print(msg, "已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
colpaper.bulk_write(operation, ordered=False)
cursor.close()
def clone_author_collection():
coll = connectTable("academic", "mag_authors")
col2 = connectTable("qiuzh", "mag_authors0409")
for i in coll.find({"id": {"$exists": True}}):
if "pubs" in i.keys():
new_document = {}
new_document["_id"] = i["id"]
new_document["pubs"] = i["pubs"]
col2.insert_one(new_document)
print(col2.find().count())
def filter_papers_by_JCR():
'''
把col1中的paper过滤到col2中，所有的paper的期刊必须都在JCR中出现过，即有field字段
:return:
'''
col1 = connectTable("qiuzh", "mag_papers0415")
col2 = connectTable("qiuzh", "mag_papers0510")
cursor = col1.find({"field": {"$exists": True}}, no_cursor_timeout=True)
for i in cursor:
col2.insert_one(i)
def filter_authors_by_papers():
'''
save authors who have new pubs in mag_authors0411
:return:
'''
col1 = connectTable("qiuzh", "mag_authors0409")
col2 = connectTable('qiuzh', "mag_authors0411")
for i in col1.find():
if i["new_pubs"]:
col2.insert_one(i)
def clone_paper_collection():
coll = connectTable("oga_one", "mag_paper")
col2 = connectTable("qiuzh", "mag_papers")
for i in coll.find({"id": {"$exists": True}}):
if "new_authors" in i.keys() and "year" in i.keys() and "references" in i.keys():
new_document = {}
new_document["_id"] = i["id"]
new_document["authors"] = i["new_authors"]
new_document["venue"] = i["new_venue"]
new_document["year"] = i["year"]
new_document["references"] = i["references"]
col2.insert_one(new_document)
print(col2.find().count())
def researchers_collaboration_network():
'''
there are some problems in researchers_con_innewcollection network, so we may use the other method to replace it
i.e create a collaboration network first.
:param begin:
:param end:
:param msg:
:return:
'''
start_time = time()
print(start_time, flush=True)
col1 = connectTable("qiuzh", "mag_papers0510")
col2 = connectTable("qiuzh", "mag_researchers0707")
col3 = connectTable("qiuzh", "coauthor_network0722")
operation = []
cursor = col2.find(no_cursor_timeout=True)
count = 0
for i in cursor:
count += 1
author_id = i["_id"]
# coauthor_times = 0
# coauthor_list = []
papers = i["new_pubs"]
for paper in papers:
paper_details = col1.find_one({"_id": paper},
no_cursor_timeout=True)
for author in paper_details["authors"]:
if author["id"] != author_id and col2.find_one(
{"_id": author["id"]}, no_cursor_timeout=True):
# coauthor_list.append({"coauthor_id": author["id"], "coauthor_time": paper_details["year"]})
operation.append(
pymongo.InsertOne({
"author_id":
author_id,
"coauthor_id":
author["id"],
"coauthor_time":
paper_details["year"],
}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col3.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col3.bulk_write(operation, ordered=False)
print("已完成", len(operation), flush=True)
print(time(), (time() - start_time), flush=True)
def add_coauthor_relation2newcollection():
'''
coauthor times and coauthor relationships
:return:
mag_authors0411:
{coauthor_counts:n}
{coauthor_list:[{year:1999,id:1000000},year:1998,id:1000001}]}
because some of the authors in the dataset have too many collaborations and exceed the maximum RAM of a document,
we store the relation in a new collection
_id:
"author_id" :
"coauthor_id":
"coauthor_time":
'''
start_time = time()
print(start_time,flush=True)
col1 = connectTable("qiuzh", "mag_papers0415")
col2 = connectTable("qiuzh", "mag_authors0411")
col3 = connectTable("qiuzh", "coauthor_network0420")
operation = []
cursor = col2.find(no_cursor_timeout=True)[3790001:]
count =0
for i in cursor:
count+=1
author_id = i["_id"]
# coauthor_times = 0
# coauthor_list = []
papers = i["new_pubs"]
for paper in papers:
paper_details = col1.find_one({"_id": paper})
# if paper_details:
# coauthor_times += (len(paper_details["authors"]) - 1)
for author in paper_details["authors"]:
if author["id"] != author_id:
# coauthor_list.append({"coauthor_id": author["id"], "coauthor_time": paper_details["year"]})
operation.append(pymongo.InsertOne(
{"author_id": author_id, "coauthor_id": author["id"], "coauthor_time": paper_details["year"],
}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col3.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col3.bulk_write(operation, ordered=False)
print("已完成",len(operation),flush=True)
print(time(), (time() - start_time), flush=True)
def filter_researchers_paper_by_authors():
'''
from mag_researchers0707(pubs>=10, academic career life >=10) to mag_researchers0810(only the author number of a
paper less than 10 will be considered in the dataset)
:param msg:
:param begin:
:param end:
:return:
this function is created in 2021.8.10
'''
# col2 = connectTable('qiuzh', "mag_researchers0707")
# col2.drop()
col1 = connectTable('qiuzh', "mag_researchers0707")
col2 = connectTable('qiuzh', "mag_researchers0810")
col_paper = connectTable("qiuzh", "mag_papers0510")
cursor = col1.find(no_cursor_timeout=True)
opt = []
count = 0
print(cursor.count())
for i in cursor:
count += 1
pubs = i["new_pubs"]
new_pubs = []
for pub in pubs:
paper = col_paper.find_one({"_id": pub["pid"]})
if len(paper["authors"]) <= 10:
new_pubs.append(pub)
opt.append(
pymongo.InsertOne({
"_id": i["_id"],
"new_pubs": new_pubs,
"pub_count": i["pub_count"],
"first_year": i["first_year"],
"last_year": i["last_year"],
"cn": i["cn"]
}))
if count % 10000 == 0:
print(len(opt))
print(count)
print("已处理:", count / 10000, flush=True)
col2.bulk_write(opt, ordered=False)
print("已写入:", count / 10000, flush=True)
opt = []
if opt:
col2.bulk_write(opt, ordered=False)
print("最终又完成", len(opt))
print(count)
cursor.close()
def filter_author_by_careerlife(begin,end,msg):
'''
:param msg:
:param begin:
:param end:
:return: pubs>=10, org exist(affiliation)
'''
col1 = connectTable('qiuzh', "mag_authors0421")
col2 = connectTable('qiuzh', "mag_authors0411")
cursor = col2.find(no_cursor_timeout=True)[begin:end]
opt =[]
for i in cursor:
if i["first_year"]-i["last_year"]>=20:
opt.append(pymongo.InsertOne({"_id":i["_id"],"new_pubs":i["new_pubs"],"pub_count":i["pub_count"],"first_year":i["first_year"],"last_year":i["last_year"]}))
col1.bulk_write(opt,ordered=False)
cursor.close()
def filter_papers_by_new_pubs():
'''
:param msg:
:param begin:
:param end:
:return: new_pubs
'''
col1 = connectTable("qiuzh","papers")
col2 = connectTable('qiuzh', "MAG_authors")
medset =set()
for i in col2.find():
for j in i.get("new_pubs"):
medset.add(j)
print(len(medset))
result=col1.delete_many({"id": {"$nin":list(medset)}})
print(result.deleted_count) # 被删除的个数
def filter_author_by_citation(begin, end,msg):
'''
:param msg: multi-process information
:param begin: i-th
:param end: i+1-th
:return: pubs counts>=5
'''
col1 = connectTable("academic", "mag_authors")
col2 = connectTable('qiuzh', "MAG_authors")
opt = []
# count = 0
for i in col1.find({"n_pubs":{"$gte":5}})[begin: end]:
a =i
opt.append(pymongo.InsertOne(i))
col2.bulk_write(opt, ordered=False)
print("线程： %s, 遍历了 %s" % (msg, len(opt)))
def filter_author_by_abstract():
'''
Some of the papers in the dataset are news and some of the authors are editor of journals, so we need to filter them by abstract
:return:
'''
col1 = connectTable("qiuzh", "mag_papers0415")
print("okay")
def find_critical_year():
'''
2020.8.31: critical_year is 1996, with 559808 rexearchers in total(more than half of the dataset)
:return:
'''
col_author = connectTable("qiuzh", "mag_researchers0810")
year_list = [
1802, 1803, 1810, 1814, 1815, 1816, 1819, 1823, 1825, 1827, 1828, 1829,
1830, 1832, 1833, 1834, 1836, 1838, 1839, 1841, 1842, 1843, 1844, 1845,
1846, 1847, 1848, 1849, 1850, 1851, 1852, 1853, 1854, 1855, 1856, 1857,
1858, 1859, 1860, 1861, 1862, 1863, 1864, 1865, 1866, 1867, 1868, 1869,
1870, 1871, 1872, 1873, 1874, 1875, 1876, 1877, 1878, 1879, 1880, 1881,
1882, 1883, 1884, 1885, 1886, 1887, 1888, 1889, 1890, 1891, 1892, 1893,
1894, 1895, 1896, 1897, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905,
1906, 1907, 1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917,
1918, 1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929,
1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940, 1941,
1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951, 1952, 1953,
1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962, 1963, 1964, 1965,
1966, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1974, 1975, 1976, 1977,
1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989,
1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013,
2014, 2015, 2016, 2017, 2018
]
# year_list = [1957, 1987]
sum = 0
for year in year_list:
researcher_number = col_author.count_documents({"first_year": year})
sum += researcher_number
print(researcher_number, sum)
if sum >= 541461:
print(year)
def author_pubs_count():
'''
author_pubs_count
:return:
'''
coll = connectTable("qiuzh", "mag_authors0510")
# coll = connectTable("qiuzh", "test1")
a = coll.aggregate([{
"$group": {
"_id": {},
"avg": {
"$avg": "$pub_count"
},
"max": {
"$max": "$pub_count"
},
"min": {
"$min": "$pub_count"
},
"sum": {
"$sum": "$pub_count"
},
}
}])
for i in a:
print(i)
def print_bsur_into_pc():
'''
in 8.30 we used this function to print the data in the txt, However, we do save the data into Bsur rather than Bsur0810
by mistake.
:return:
'''
col1 = connectTable('qiuzh', "mag_researchers0810")
DI = []
KI = []
SI = []
for author in col1.find():
d_i = author["bsur"]
k_i = author["ifdis"]
s_i = author["iftop"]
DI.append(d_i)
KI.append(k_i)
SI.append(s_i)
print("list has loaded")
data = open("C:/Users/qzh/PycharmProjects/MAG/datafile/Bsur0810.txt", "w+")
for j in range(len(DI)):
print(DI[j], file=data)
data.close()
data = open("C:/Users/qzh/PycharmProjects/MAG/datafile/Ifdis0810.txt",
"w+")
for j in range(len(KI)):
print(KI[j], file=data)
data.close()
data = open("C:/Users/qzh/PycharmProjects/MAG/datafile/Iftop0810.txt",
"w+")
for j in range(len(SI)):
print(SI[j], file=data)
data.close()
def calculate_coauthor_times2():
'''
this version is appropriate for mag_authors0510
this function is not finished
:return:
'''
start_time = time()
print(start_time)
col1 = connectTable("qiuzh", "mag_authors0411")
operation = []
count=0
cursor = col1.find(no_cursor_timeout=True)
for i in cursor:
count+=1
author_id = i["_id"]
coauthor_times = col1.count({"author_id": author_id})
operation.append(pymongo.UpdateOne({"_id": author_id}, {"$set": {"coauthor_times": coauthor_times}}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col1.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col1.bulk_write(operation, ordered=False)
cursor.close()
print(time(), (time() - start_time))
def boot_strap(P_d):
col_author = connectTable("qiuzh", "researchers0810_trainingset")
cursor = col_author.find(no_cursor_timeout=True)
count = 0
operation = []
for author in cursor:
count += 1
coauthor_times = author["new_con"]
author_id = author["_id"]
d_i_list = np.random.binomial(coauthor_times, P_d, 20)
surprisal_list = []
for di in d_i_list:
P0 = stats.binom.sf(di - 1, coauthor_times, P_d)
surprisal_list.append(-math.log(P0))
S = np.mean(surprisal_list)
operation.append(
pymongo.UpdateOne({"_id": author_id}, {"$set": {
"bsur": S
}}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col_author.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col_author.bulk_write(operation, ordered=False)
print("又写入并完成", len(operation))
cursor.close()
print(col_author.count_documents({"sur": -6}))
print(col_author.count_documents({"dn": -1}))
print(col_author.count_documents({"bsur": -6}))
def find_discoverer(maxbsur):
col_author = connectTable("qiuzh", "researchers0810_trainingset")
cursor = col_author.find(no_cursor_timeout=True)
count = 0
operation = []
for author in cursor:
count += 1
sur = author["sur"]
author_id = author["_id"]
if sur >= 0 and sur < maxbsur:
operation.append(
pymongo.UpdateOne({"_id": author_id}, {"$set": {
"ifdis": 0
}}))
else:
operation.append(
pymongo.UpdateOne({"_id": author_id}, {"$set": {
"ifdis": 1
}}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col_author.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col_author.bulk_write(operation, ordered=False)
print("又写入并完成", len(operation))
cursor.close()
def initialize_surprisal():
col_author = connectTable("qiuzh", "researchers0810_trainingset")
cursor = col_author.find(no_cursor_timeout=True)
# researcher_number = cursor.count()
# print(researcher_number)
count = 0
operation = []
for author in cursor:
count += 1
operation.append(
pymongo.UpdateOne({"_id": author["_id"]},
{"$set": {
"sur": -6,
"bsur": -6
}}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col_author.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
if operation:
col_author.bulk_write(operation, ordered=False)
print("finished")
cursor.close()
print(count)
print(col_author.find({"dn": -1}, no_cursor_timeout=True).count())
def initialize_discover_number():
'''
this function is used in 2021.8.12 in mag_researchers0810
in 2021.9.1 we used this function in researchers0810_trainingset
:return:
'''
col_author = connectTable("qiuzh", "researchers0810_trainingset")
cursor = col_author.find(no_cursor_timeout=True)
# researcher_number = cursor.count()
# print(researcher_number)
count = 0
operation = []
for author in cursor:
count += 1
operation.append(
pymongo.UpdateOne({"_id": author["_id"]}, {"$set": {
"dn": -1
}}))
if count % 10000 == 0:
print("已处理:", count / 10000, flush=True)
col_author.bulk_write(operation, ordered=False)
print("已写入:", count / 10000, flush=True)
operation = []
if operation:
col_author.bulk_write(operation, ordered=False)
print("finished")
cursor.close()
print(count)
print(col_author.find({"dn": -1}, no_cursor_timeout=True).count())
def new_pub_count(begin, end, msg):
col_author = connectTable("qiuzh", "researchers0810_trainingset")
count = 0
operation = []
cursor = col_author.find(no_cursor_timeout=True)[begin:end]
for author in cursor:
count += 1
author_id = author["_id"]
pub_count = 0
for paper in author["new_pubs"]:
if paper["year"] <= 1996:
pub_count += 1
operation.append(
pymongo.UpdateOne({"_id": author_id},
{"$set": {
"pub_count": pub_count
}}))
if count % 10000 == 0:
print(msg, "已处理:", count / 10000, flush=True)
col_author.bulk_write(operation, ordered=False)
print(msg, "已写入:", count / 10000, flush=True)
operation = []
print(time(), flush=True)
if operation:
col_author.bulk_write(operation, ordered=False)
cursor.close()
def author_first_year_distribution():
'''
:return:
'''
col = connectTable("qiuzh", "mag_authors0510")
yearlist = col.distinct("first_year")
print(yearlist)
def delete_coauthor_counts():
col = connectTable('qiuzh', "mag_authors0411")
# cursor = col.find({"coauthor_counts":{"$exists": True}},no_cursor_timeout=True)[begin:end]
# for i in cursor:
# _id = i.get("_id")
# col.update_one({"_id":_id}, {"$unset": {"new_pubs": 1}},False,True)
col.update_many({"coauthor_counts": {"$exists": True}}, {"$unset": {"coauthor_counts": 1, "coauthor": 1}})
# cursor.close()
print("yes okay")
def author_pubs_number():
mycol = connectTable("qiuzh", "mag_authors0510")
for i in mycol.find():
author_id = i["_id"]
pub_number = len(i["new_pubs"])
mycol.update_one({"_id": author_id},
{"$set": {
"pub_count": pub_number
}})
