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import re
from typing import Optional
DOI_REGEX = re.compile(r"^10.\d{3,6}/\S+$")
def clean_doi(raw: Optional[str]) -> Optional[str]:
"""
Removes any:
- padding whitespace
- 'doi:' prefix
- URL prefix
Does not try to un-URL-encode
Returns None if not a valid DOI
"""
if not raw:
return None
raw = raw.strip().lower()
if "\u2013" in raw:
# Do not attempt to normalize "en dash" and since FC does not allow
# unicode in DOI, treat this as invalid.
return None
if len(raw.split()) != 1:
return None
if not "10." in raw:
return None
if not raw.startswith("10."):
raw = raw[raw.find("10."):]
if raw[7:9] == "//":
raw = raw[:8] + raw[9:]
# fatcatd uses same REGEX, but Rust regex rejects these characters, while
# python doesn't. DOIs are syntaxtually valid, but very likely to be typos;
# for now filter them out.
for c in ("¬",):
if c in raw:
return None
if not raw.startswith("10."):
return None
if not DOI_REGEX.fullmatch(raw):
return None
# will likely want to expand DOI_REGEX to exclude non-ASCII characters, but
# for now block specific characters so we can get PubMed importer running
# again.
if "ä" in raw:
return None
return raw
def test_clean_doi() -> None:
assert clean_doi(None) == None
assert clean_doi("") == None
assert clean_doi("asdf") == None
assert clean_doi("10.123") == None
assert clean_doi("10.1234/asdf ") == "10.1234/asdf"
assert clean_doi("10.1234/ASdf ") == "10.1234/asdf"
assert clean_doi("10.1037//0002-9432.72.1.50") == "10.1037/0002-9432.72.1.50"
assert clean_doi("10.1037/0002-9432.72.1.50") == "10.1037/0002-9432.72.1.50"
assert clean_doi("10.23750/abm.v88i2 -s.6506") == None
assert clean_doi("10.17167/mksz.2017.2.129–155") == None
assert clean_doi("http://doi.org/10.1234/asdf ") == "10.1234/asdf"
assert clean_doi("https://dx.doi.org/10.1234/asdf ") == "10.1234/asdf"
assert clean_doi("doi:10.1234/asdf ") == "10.1234/asdf"
assert clean_doi("doi:10.1234/ asdf ") == None
assert clean_doi("10.4149/gpb¬_2017042") == None # "logical negation" character
assert (
clean_doi("10.6002/ect.2020.häyry") == None
) # this example via pubmed (pmid:32519616)
# GROBID mangled DOI
assert clean_doi("21924DOI10.1234/asdf ") == "10.1234/asdf"
def clean_pmcid(raw: Optional[str]) -> Optional[str]:
if not raw:
return None
raw = raw.strip().upper()
if len(raw.split()) != 1:
return None
if raw.startswith("PMC") and raw[3:] and raw[3:].isdigit():
return raw
return None
def test_clean_pmcid() -> None:
assert clean_pmcid("10.1234/asdf ") == None
assert clean_pmcid("") == None
assert clean_pmcid("1 2") == None
assert clean_pmcid(None) == None
assert clean_pmcid("PMC123") == "PMC123"
assert clean_pmcid("pmc123") == "PMC123"
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