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"""
A bunch of helpers to parse and normalize strings: external identifiers,
free-form input, titles, etc.
"""
import re
DOI_REGEX = re.compile(r"^10.\d{3,6}/\S+$")
def clean_doi(raw):
"""
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()
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 raw.startswith("doi:"):
raw = raw[4:]
if raw.startswith("http://"):
raw = raw[7:]
if raw.startswith("https://"):
raw = raw[8:]
if raw.startswith("doi.org/"):
raw = raw[8:]
if raw.startswith("dx.doi.org/"):
raw = raw[11:]
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 or '\u200e' in raw:
return None
return raw
def test_clean_doi():
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)
assert clean_doi("10.30466/vrf.2019.98547.2350\u200e") == None
ARXIV_ID_REGEX = re.compile(r"^(\d{4}.\d{4,5}|[a-z\-]+(\.[A-Z]{2})?/\d{7})(v\d+)?$")
def clean_arxiv_id(raw):
"""
Removes any:
- 'arxiv:' prefix
Works with versioned or un-versioned arxiv identifiers.
"""
if not raw:
return None
raw = raw.strip()
if raw.lower().startswith("arxiv:"):
raw = raw[6:]
if raw.lower().startswith("https://arxiv.org/abs/"):
raw = raw[22:]
if not ARXIV_ID_REGEX.fullmatch(raw):
return None
return raw
def test_clean_arxiv_id():
assert clean_arxiv_id("0806.2878v1") == "0806.2878v1"
assert clean_arxiv_id("0806.2878") == "0806.2878"
assert clean_arxiv_id("1501.00001v1") == "1501.00001v1"
assert clean_arxiv_id("1501.00001") == "1501.00001"
assert clean_arxiv_id("hep-th/9901001v1") == "hep-th/9901001v1"
assert clean_arxiv_id("hep-th/9901001") == "hep-th/9901001"
assert clean_arxiv_id("math.CA/0611800v2") == "math.CA/0611800v2"
assert clean_arxiv_id("math.CA/0611800") == "math.CA/0611800"
assert clean_arxiv_id("0806.2878v1 ") == "0806.2878v1"
assert clean_arxiv_id("https://arxiv.org/abs/0806.2878v1") == "0806.2878v1"
assert clean_arxiv_id("arxiv:0806.2878v1") == "0806.2878v1"
assert clean_arxiv_id("arXiv:0806.2878v1") == "0806.2878v1"
assert clean_arxiv_id("hep-TH/9901001v1") == None
assert clean_arxiv_id("hßp-th/9901001v1") == None
assert clean_arxiv_id("math.CA/06l1800v2") == None
assert clean_arxiv_id("mßth.ca/0611800v2") == None
assert clean_arxiv_id("MATH.CA/0611800v2") == None
assert clean_arxiv_id("0806.2878v23") == "0806.2878v23" # ?
assert clean_arxiv_id("0806.2878v") == None
assert clean_arxiv_id("0806.2878") == "0806.2878"
assert clean_arxiv_id("006.2878v1") == None
assert clean_arxiv_id("0806.v1") == None
assert clean_arxiv_id("08062878v1") == None
def clean_pmid(raw):
if not raw:
return None
raw = raw.strip()
if len(raw.split()) != 1:
return None
if raw.isdigit():
return raw
return None
def test_clean_pmid():
assert clean_pmid("1234") == "1234"
assert clean_pmid("1234 ") == "1234"
assert clean_pmid("PMC123") == None
assert clean_sha1("qfba3") == None
assert clean_sha1("") == None
def clean_pmcid(raw):
if not raw:
return None
raw = raw.strip()
if len(raw.split()) != 1:
return None
if raw.startswith("PMC") and raw[3:] and raw[3:].isdigit():
return raw
return None
def clean_sha1(raw):
if not raw:
return None
raw = raw.strip().lower()
if len(raw.split()) != 1:
return None
if len(raw) != 40:
return None
for c in raw:
if c not in "0123456789abcdef":
return None
return raw
def test_clean_sha1():
assert clean_sha1("0fba3fba0e1937aa0297de3836b768b5dfb23d7b") == "0fba3fba0e1937aa0297de3836b768b5dfb23d7b"
assert clean_sha1("0fba3fba0e1937aa0297de3836b768b5dfb23d7b ") == "0fba3fba0e1937aa0297de3836b768b5dfb23d7b"
assert clean_sha1("fba3fba0e1937aa0297de3836b768b5dfb23d7b") == None
assert clean_sha1("qfba3fba0e1937aa0297de3836b768b5dfb23d7b") == None
assert clean_sha1("0fba3fb a0e1937aa0297de3836b768b5dfb23d7b") == None
def clean_sha256(raw):
raw = raw.strip().lower()
if len(raw.split()) != 1:
return None
if len(raw) != 64:
return None
for c in raw:
if c not in "0123456789abcdef":
return None
return raw
def test_clean_sha256():
assert clean_sha256("6cc853f2ae75696b2e45f476c76b946b0fc2df7c52bb38287cb074aceb77bc7f") == "6cc853f2ae75696b2e45f476c76b946b0fc2df7c52bb38287cb074aceb77bc7f"
assert clean_sha256("0fba3fba0e1937aa0297de3836b768b5dfb23d7b") == None
ISSN_REGEX = re.compile(r"^\d{4}-\d{3}[0-9X]$")
def clean_issn(raw):
if not raw:
return None
raw = raw.strip().upper()
if len(raw) != 9:
return None
if not ISSN_REGEX.fullmatch(raw):
return None
return raw
def test_clean_issn():
assert clean_issn("1234-4567") == "1234-4567"
assert clean_issn("1234-456X") == "1234-456X"
assert clean_issn("134-4567") == None
assert clean_issn("123X-4567") == None
ISBN13_REGEX = re.compile(r"^97(?:8|9)-\d{1,5}-\d{1,7}-\d{1,6}-\d$")
def clean_isbn13(raw):
if not raw:
return None
raw = raw.strip()
if not ISBN13_REGEX.fullmatch(raw):
return None
return raw
def test_clean_isbn13():
assert clean_isbn13("978-1-56619-909-4") == "978-1-56619-909-4"
assert clean_isbn13("978-1-4028-9462-6") == "978-1-4028-9462-6"
assert clean_isbn13("978-1-56619-909-4 ") == "978-1-56619-909-4"
assert clean_isbn13("9781566199094") == None
ORCID_REGEX = re.compile(r"^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$")
def clean_orcid(raw):
if not raw:
return None
raw = raw.strip()
if not ORCID_REGEX.fullmatch(raw):
return None
return raw
def test_clean_orcid():
assert clean_orcid("0123-4567-3456-6789") == "0123-4567-3456-6789"
assert clean_orcid("0123-4567-3456-678X") == "0123-4567-3456-678X"
assert clean_orcid("0123-4567-3456-6789 ") == "0123-4567-3456-6789"
assert clean_orcid("01234567-3456-6780") == None
assert clean_orcid("0x23-4567-3456-6780") == None
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