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helper.py
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helper.py
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import json
import re
from dataclasses import dataclass
from pathlib import Path
import clipboard
import requests
from SPARQLWrapper import JSON, SPARQLWrapper
from wdcuration import add_key
from .dictionaries.all import dicts
from .wikidata_lookup import search_wikidata
HERE = Path(__file__).parent.resolve()
DICTIONARIES_PATH = HERE.joinpath("dictionaries")
DEGREE_PATH = DICTIONARIES_PATH.joinpath("degree.json")
def render_orcid_qs(orcid):
"""
Import info from ORCID for Wikidata.
Args:
orcid: The ORCID of the researcher to reconcile to Wikidata.
"""
# From https://pub.orcid.org/v3.0/#!/Public_API_v2.0/viewRecord
url = "https://pub.orcid.org/v2.0/"
header = {"Accept": "application/json"}
payload = {"orcid": orcid}
r = requests.get(f"{url}{orcid}", headers=header)
data = r.json()
with open("sample.json", "w+") as f:
f.write(json.dumps(data, indent=4))
personal_data = data["person"]
employment_data = data["activities-summary"]["employments"]["employment-summary"]
education_data = data["activities-summary"]["educations"]["education-summary"]
publication_data = data["activities-summary"]["works"]
first_name = personal_data["name"]["given-names"]["value"]
last_name = personal_data["name"]["family-name"]["value"]
employment_institutions = get_organization_list(employment_data)
education_entries = get_education_info(education_data)
s = lookup_id(orcid, property="P496", default="LAST")
ref = f'|S854|"https://orcid.org/{str(orcid)}"'
if s == "LAST":
qs = f"""CREATE
{s}|Len|"{first_name} {last_name}"
{s}|Den|"researcher"
"""
else:
qs = ""
qs = (
qs
+ f"""
{s}|P31|Q5{ref}
{s}|P106|Q1650915{ref}
{s}|P496|"{orcid}"{ref}
"""
)
property_id = "P108"
key = "institutions"
target_list = employment_institutions
qs = process_item(
qs,
property_id,
original_dict=key,
target_list=target_list,
subject_qid=s,
ref=ref,
)
qs = process_education_entries(
qs,
subject_qid=s,
ref=ref,
education_entries=education_entries,
property_id="P69",
)
return qs
@dataclass
class EducationEntry:
"""Class for capturing the info for an education entry on ORCID."""
institution: str
degree: str
start_date: str = None
end_date: str = None
def process_item(
qs,
property_id,
original_dict,
target_list,
subject_qid,
ref,
qualifier_nested_dictionary={},
):
global dicts
for target_item in target_list:
if re.findall("Q[0-9]*", target_item):
qid = target_item
else:
qid = get_qid_for_item(original_dict, target_item)
qs = (
qs
+ f"""
{subject_qid}|{property_id}|{qid}"""
)
if qualifier_nested_dictionary != {}:
qualifier_pairs = qualifier_nested_dictionary[target_item]
for key, value in qualifier_pairs.items():
qs = qs + f"|{key}|{value}" + f"{ref}"
else:
qs = qs + f"{ref}"
return qs
def get_qid_for_item(original_dict_name, target_item):
"""
Looks up the qid given a key using global dict of dicts.
If it is not present, it lets the user update the dict.
Args:
original_dict_name (str): The dict name
target_item (str): The string to lookup in the dict
Returns:
qid:str
"""
if target_item not in dicts[original_dict_name]:
add_key(dicts[original_dict_name], target_item)
with DICTIONARIES_PATH.joinpath(f"{original_dict_name}.json").open("w") as f:
f.write(json.dumps(dicts[original_dict_name], indent=4, sort_keys=True))
qid = dicts[original_dict_name][target_item]
return qid
def lookup_id(id, property, default):
"""
Looks up a foreign ID on Wikidata based on its specific property.
"""
sparql = SPARQLWrapper(
"https://query.wikidata.org/sparql",
agent="PyORCIDator (https://github.com/lubianat/pyorcidator)",
)
query = f"""
SELECT ?item ?itemLabel
WHERE
{{
?item wdt:{property} "{id}" .
}}
"""
sparql.setQuery(query)
sparql.setReturnFormat(JSON)
results = sparql.query().convert()
bindings = results["results"]["bindings"]
if len(bindings) == 1:
item = bindings[0]["item"]["value"].split("/")[-1]
return item
else:
return default
def get_organization_list(data):
organization_list = []
for a in data:
a = a["organization"]
name = a["name"]
if a["disambiguated-organization"] is None:
continue
if a["disambiguated-organization"]["disambiguation-source"] == "GRID":
grid = a["disambiguated-organization"]["disambiguated-organization-identifier"]
id = lookup_id(grid, "P2427", name)
name = id
organization_list.append(name)
return organization_list
def get_date(entry, start_or_end="start"):
date = entry[f"{start_or_end}-date"]
if date is None:
return ""
month = "00"
day = "00"
if date["year"] is not None:
year = date["year"]["value"]
precision = 9
if date["month"] is not None:
month = date["month"]["value"]
precision = 10
if date["day"] is not None:
day = date["day"]["value"]
precision = 11
return f"+{year}-{month}-{day}T00:00:00Z/{str(precision)}"
def get_education_info(data):
organization_list = []
for a in data:
qualifiers = {}
title = a["role-title"]
degree_qid = get_qid_for_item("degree", title)
start_date = get_date(a, "start")
end_date = get_date(a, "end")
a = a["organization"]
name = a["name"]
if (
a["disambiguated-organization"]
and "disambiguation-source" in a["disambiguated-organization"]
and a["disambiguated-organization"].get("disambiguation-source") == "GRID"
):
grid = a["disambiguated-organization"]["disambiguated-organization-identifier"]
institution_qid = lookup_id(grid, "P2427", name)
else:
institution_qid = get_qid_for_item("institutions", name)
entry = EducationEntry(
degree=degree_qid,
institution=institution_qid,
start_date=start_date,
end_date=end_date,
)
organization_list.append(entry)
return organization_list
def process_education_entries(qs, subject_qid, ref, education_entries, property_id="P69"):
# Quickstatements fails in the case of same institution for multliple degrees.
# See https://www.wikidata.org/wiki/Help:QuickStatements#Limitation
for entry in education_entries:
if entry.start_date == "":
qs = (
qs
+ f"""
{subject_qid}|{property_id}|{entry.institution}|P512|{entry.degree}{ref}"""
)
else:
qs = (
qs
+ f"""
{subject_qid}|{property_id}|{entry.institution}|P512|{entry.degree}|P580|{entry.start_date}|P582|{entry.end_date}{ref}"""
)
return qs
def get_paper_dois(group_of_works_from_orcid):
""" """
dois = []
for work in group_of_works_from_orcid:
for external_id in work["external-ids"]["external-id"]:
if external_id["external-id-type"] == "doi":
dois.append(external_id["external-id-value"])
print(dois)
return dois