def get_publications(
sup_cur: db.Cursor,
permitted_people: Dict[int, Person]
) -> Mapping[str, Publication]:
print("Gathering publications")
authorships = db.get_pubmed_authorships(sup_cur)
pubs = db.get_pubmed_publications(sup_cur)
publications = {}
for pmid, xml in pubs.items():
if pmid not in authorships:
continue
try:
pub = Publication.from_pubmed(xml)
assert pub and pub.pmid == pmid
for author in authorships[pmid]:
if author in permitted_people:
pub.add_author(author)
publications[pmid] = pub
except Exception:
traceback.print_exc()
print(f"Skipping publication {pmid}")
return publications
def add_developers(sup_cur: db.Cursor) -> None:
pmids = set(tools.MetabolomicsToolsWiki.pmids())
total = len(pmids)
if total == 0:
return
publications = db.get_pubmed_publications(sup_cur, pmids)
pmids = pmids.intersection(publications.keys())
print(f"Found {len(pmids)} of {total} tools-related publications in the "
"Supplemental database.")
if len(pmids) == 0:
return
for pmid in pmids:
author_list = parse_author_list(publications[pmid])
for author in author_list:
forename = author.findtext("ForeName", "").strip()
lastname = author.findtext("LastName", "").strip()
if not forename:
print(f"PMID {pmid}: missing forename of author {lastname}")
continue
if not lastname:
print(f"PMID {pmid}: missing surname of author {forename}")
continue
matches = list(db.get_person(sup_cur, forename, lastname))
if len(matches) > 1:
print(f"PMID {pmid}: WARNING! Found {len(matches)} people "
f" named {forename} {lastname}: {matches}")
continue
if matches:
pid = matches[0]
print(f"PMID {pmid}: found {forename} {lastname}: {pid}")
else:
pid = db.add_person(sup_cur, forename, lastname, "", "")
if not pid:
print(f"PMID {pmid}: WARNING failed to add person: "
f"{forename} {lastname}")
continue
print(f"PMID {pmid}: added {forename} {lastname}: {pid}")
affiliation_list = author.findall(".//Affiliation")
for element in affiliation_list:
affiliation = element.text
if affiliation is None or affiliation.strip() == '':
continue
print(f"PMID {pmid}: affiliation for {forename} {lastname}"
f": {affiliation.strip()}")
return
def get_authors_pmid(sup_cur: db.Cursor, pmid: str) -> List[Dict[str, str]]:
try:
authors = []
pubs = db.get_pubmed_publications(sup_cur, pmids=[pmid])
if pmid not in pubs:
print(f'PMID {pmid}: Could not find PubMed data')
return []
author_list = prefill.parse_author_list(pubs[pmid])
for author in author_list:
forename = author.findtext('ForeName', '').strip()
surname = author.findtext('LastName', '').strip()
auth = {'name': f'{forename} {surname}'.strip()}
authors.append(auth)
return authors
except Exception:
traceback.print_exc()
print(f'Error parsing PubMed Data for tool with PMID {pmid}')
return []