Adding script to add orcids to externalcontacts

This script uses the publications to pull in ORCIDs using OpenAlex and article DOIs where available.  These new ORCIDs are then added to the table `ndb.externalcontacts` with identifier `7`.

The script can be run using `uv run get_orcid.py`.

Author: SimonGoring

Proposals/orcids/.python-version

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+3.12

Proposals/orcids/README.md

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+# Adding ORCIDs to Neotoma
+
+Adding ORCIDs takes several steps. We need to create a table that links individuals to `contacts`.
+
+```sql
+CREATE TABLE ndb.externalcontacts (
+    contactid INT references ndb.contacts (contactid),
+    identifier text,
+    extdatabaseid INT references ndb.externaldatabases (extdatabaseid),
+    UNIQUE(contactid, identifier, extdatabaseid));
+```
+
+Once this table is created, we can search for ORCIDs and insert them into the database, tying them to publications and users.
+
+The script 

Proposals/orcids/get_orcids.py

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+# We'll read in the `outputs.csv` file, and then for each row, update the DOI column.
+import psycopg2
+import dotenv
+import os
+import json
+import requests
+import re
+from pyalex import config, Works, Authors, Topics
+
+config.max_retries = 0
+config.retry_backoff_factor = 0.1
+config.retry_http_codes = [429, 500, 503]
+config.email = "goring@wisc.edu"
+
+dotenv.load_dotenv()
+
+dbauth = json.loads(os.getenv('DBAUTH'))
+
+conn = psycopg2.connect(**dbauth, connect_timeout=5)
+
+def get_publications(limit:int=100000) -> list:
+    url = 'https://api.neotomadb.org/v2.0/data/publications'
+    all_pub = requests.get(url,
+                           params = {'limit': limit})
+    if all_pub.status_code == 200:
+        pub_data = json.loads(all_pub.content).get('data').get('result')
+    else:
+        return None
+    doi_set = list()
+    for i in pub_data:
+        doi = i.get('publication').get('doi')
+        pubid = i.get('publication').get('publicationid', '')
+        if doi is not None:
+            doi_set.append({'doi': doi, 'publicationid': pubid})
+    return doi_set
+
+def check_authors(doi:str):
+    full_doi = "https://doi.org/" + doi
+    alex_result = Works()[full_doi]
+    return alex_result
+
+def get_pub_auth(pubid) -> list:
+    query = """
+        SELECT pa.* 
+        FROM ndb.publicationauthors AS pa
+        LEFT JOIN ndb.externalcontacts AS exct ON exct.contactid = pa.contactid
+        WHERE publicationid = %(pubid)s AND exct.contactid IS NULL;"""
+    with conn.cursor() as cur:
+        cur.execute(query, {'pubid': pubid})
+        result = cur.fetchall()
+    return result
+
+def align_pubs(doi_set:dict) -> dict:
+    pub_auth = get_pub_auth(doi_set['publicationid'])
+    if len(pub_auth) == 0:
+        return []
+    try:
+        alex_res = check_authors(doi_set['doi'])
+    except Exception:
+        return []
+    authors = alex_res['authorships']
+    author_set = []
+    for i in pub_auth:
+        paper_auth = {'contactid': i[6],
+                      'name': None,
+                      'orcid': None}
+        orcids = [j['author']['orcid'] for j in authors if re.search(i[3], j['raw_author_name'])]
+        name = [j['raw_author_name'] for j in authors if re.search(i[3], j['raw_author_name'])]
+        if len(orcids) > 0:
+            paper_auth['orcid'] = orcids[0]
+        if len(name) > 0:
+            paper_auth['name'] = name[0]
+        author_set.append(paper_auth)
+    return author_set
+
+def insert_orcid(author):
+    query = """
+    INSERT INTO ndb.externalcontacts(contactid, identifier, extdatabaseid)
+    VALUES (%(contactid)s, %(orcid)s, 7)
+    ON CONFLICT (contactid, identifier, extdatabaseid) DO NOTHING;"""
+    with conn.cursor() as cur:
+        cur.execute(query, author)
+    conn.commit()
+    return None
+
+all_pubs = get_publications(100000)
+
+find_authors = []
+for i in all_pubs:
+    new_outcome = align_pubs(i)
+    for j in new_outcome:
+        if j['orcid']:
+            print(f"Found ORCID for {j['name']} through OpenAlex.")
+            insert_orcid(j)
+

Proposals/orcids/pyproject.toml

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+[project]
+name = "orcids"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "psycopg2>=2.9.10",
+    "pyalex>=0.15.1",
+    "python-dotenv>=1.0.1",
+    "requests>=2.32.3",
+]