import requests
import pandas as pd
from io import StringIO
from difflib import SequenceMatcher
import urllib.parse
import time
import sys
def getPoints(liste):
return liste[2]
class disambiguate:
def __init__(self, infoDic, nameDepth = 20, worksDepth = 20):
print(nameDepth, worksDepth,file=sys.stderr)
self.timeBetweenrequest = 0.01
self.version = "v3.0"
self.nameDepth = nameDepth
self.worksDepth = worksDepth
self.infoDic = {}
self.extractInfoDic(infoDic)
def getDfFromName(self,name):
url = "https://pub.orcid.org/v3.0/csv-search/?q="+urllib.parse.quote("(given-and-family-names:"+name+")")
response = requests.get(url,headers={'Accept':'text/csv'})
df = pd.read_csv(StringIO(str(response.content,'utf-8')))
return df
def getWorksFromOrcid(self,orcid):
url = "https://pub.orcid.org/"+self.version+"/"+orcid+"/works"
response = requests.get(url,headers={'Accept':'application/orcid+json'})
works = response.json().get("group")
return works
def getCoAuthorsFromPutcode(self,putcode,orcid):
url = "https://pub.orcid.org/"+self.version+"/"+orcid+"/work/"+str(putcode)
response = requests.get(url,headers={'Accept':'application/orcid+json'})
contributors = response.json().get("contributors")
try:
coAuthors = [contributor["credit-name"]['value'] for contributor in contributors.get("contributor")]
except:
coAuthors = ""
return coAuthors
def extractInfoDic(self,dic):
self.infoDic["firstName"] = dic["firstName"]
self.infoDic["lastName"] = dic["lastName"]
if "email" in dic:
self.infoDic["email"] = dic["email"]
if "affiliations" in dic:
self.infoDic["affiliations"] = dic["affiliations"]
if "titles" in dic:
self.infoDic["titles"] = dic["titles"]
if "coAuthors" in dic:
self.infoDic["coAuthors"] = dic["coAuthors"]
def extractDfInfos(self,df):
infos = []
for i in range(self.nameDepth):
dic = {}
dic["firstName"] = str(df["given-names"][i])
dic["lastName"] = str(df["family-name"][i])
dic["email"] = str(df["email"][i])
try:
dic["affiliations"] = df["current-institution-affiliation-name"][i].split(",")
except:
dic["affiliations"] = []
try:
dic["affiliations"] += df["past-institution-affiliation-name"][i].split(",")
except:
pass
dic["orcid"] = df["orcid"][i]
infos.append(dic)
return infos
def extractInfoFromWorks(self,works):
dic = { "putcode" : [],
"title" : [],
"publicationDate" : [],
"journal" : [],
"externalIds" : []}
for i,work in enumerate(works):
if i > self.worksDepth:
break
workSummary = work.get('work-summary')
for ws in workSummary :
dic["putcode"].append(ws.get("put-code"))
dic["title"].append(ws.get("title").get('title').get("value"))
try:
dic["publicationDate"].append(ws.get("publication-date").get("year").get('value'))
except:
dic["publicationDate"].append("Err")
try:
dic["journal"].append(ws.get("journal-title"))
except:
dic["journal"].append("Err")
try:
dic["externalIds"].append([external_id['external-id-value'] for external_id in ws.get("external-ids")["external-id"]])
except:
dic["externalIds"].append(["Err"])
return dic
def splitFirstName(self,name):
choice = []
nameSplit = name.lower().split(" ")
try:
while True:
nameSplit.remove("")
except ValueError:
pass
if len(nameSplit) > 2:
nameSplit = [" ".join(nameSplit[:-1]),nameSplit[-1]]
choice.append(name.lower())
choice.append(nameSplit[1]+" "+nameSplit[0])
fnSplit = nameSplit[0].split("-") #composed firstname with - in it
if len(fnSplit) > 1: #composed firstname with - in it
choice.append(nameSplit[1]+", "+fnSplit[0][0]+".-"+fnSplit[1][0]+".")
choice.append(nameSplit[1]+", "+fnSplit[0][0]+"."+fnSplit[1][0]+".")
else: #composed first name with space in it
fnSplit = nameSplit[0].split(" ")
if len(fnSplit) > 1:
choice.append(nameSplit[1]+", "+fnSplit[0]+".-"+fnSplit[1][0]+".") #lastname, Jaa.-P.
choice.append(nameSplit[1]+", "+fnSplit[0]+" "+fnSplit[1][0]+".")#lastname, Jaa P.
choice.append(nameSplit[1]+", "+fnSplit[0][0]+"."+fnSplit[1][0]+".") #lastname, Jaa.P.
choice.append(fnSplit[0]+" "+fnSplit[1][0]+". "+nameSplit[1])#Jaa P. lastname
choice.append(fnSplit[0][0]+"."+fnSplit[1][0]+". "+nameSplit[1])#J.P. lastname
choice.append(fnSplit[0][0]+fnSplit[1][0]+". "+nameSplit[1])#JP. lastname
else:
choice.append(nameSplit[1]+", "+nameSplit[0][0]+".")
if len(fnSplit) == 1: #composed first name with space in it
fnSplit = nameSplit[0].split("-")
return choice
def checkEmail(self,email):
for em in self.infoDic["email"]:
if em == email:
return True,em
return False,0
def disambiguation(self):
df = self.getDfFromName(self.infoDic["firstName"]+"+AND+"+self.infoDic["lastName"])
time.sleep(self.timeBetweenrequest)
personsInfos = self.extractDfInfos(df)
for personInfos in personsInfos:
orcid = personInfos["orcid"]
matchArg = []
points = 0
if "email" in self.infoDic: #check email
end,em = self.checkEmail(personInfos["email"])
if end:
return [[orcid,["Email "+em],100]]
works = self.getWorksFromOrcid(orcid)
time.sleep(self.timeBetweenrequest)
worksInfo = self.extractInfoFromWorks(works)
if "titles" in self.infoDic: #check title
for title in self.infoDic["titles"]:
for tit in [title.lower() for title in worksInfo["title"]]:
ratio = SequenceMatcher(None, title.lower(), tit).ratio() #check similarity between title
if ratio > 0.7:
return [[orcid,["title "+tit],100]]
if "coAuthors" in self.infoDic: #check coAuthors
authorsPutcode = []
for putcode in worksInfo["putcode"]:
authorsPutcode += self.getCoAuthorsFromPutcode(putcode,orcid)
time.sleep(self.timeBetweenrequest)
authors = list(set(authorsPutcode))
for author in self.infoDic["coAuthors"]:
choices = self.splitFirstName(author)
for choice in choices:
if choice in [auth.lower() for auth in authors]:
return [[orcid,["Co-authors "+choice],100]]
if "affiliations" in self.infoDic: #check affiliations
for affiliation in self.infoDic["affiliations"]:
if affiliation.lower() in [aff.lower() for aff in personInfos["affiliations"]]:
matchArg.append("Affiliation "+affiliation)
points += 10
#check first and last name
if self.infoDic["lastName"].lower() == personInfos["lastName"].lower():
if self.infoDic["firstName"].lower() == personInfos["firstName"].lower():
points += 10
matchArg.append("Match First+LastName ")
elif self.infoDic["firstName"].lower()[0] == personInfos["firstName"].lower()[0]:
points += 7
matchArg.append("Match FirstName First Letter+LastName ")
else:
points += 5
matchArg.append("Match LastName ")
personInfos["points"] = points
personInfos["matchArg"] = matchArg
#check first and last name
finalReturn = []
for personInfos in personsInfos:
if personInfos["points"] != 0:
finalReturn.append([personInfos["orcid"],personInfos["matchArg"],personInfos["points"]])
finalReturn.sort(key=getPoints,reverse=True)
return finalReturn
