diff options
| -rw-r--r-- | fuzzycat/grobid_unstructured.py | 3 | ||||
| -rw-r--r-- | fuzzycat/simple.py | 3 | ||||
| -rw-r--r-- | fuzzycat/utils.py | 14 | ||||
| -rw-r--r-- | fuzzycat/verify.py | 6 | ||||
| -rw-r--r-- | tests/test_utils.py | 15 |
5 files changed, 35 insertions, 6 deletions
diff --git a/fuzzycat/grobid_unstructured.py b/fuzzycat/grobid_unstructured.py index 79c39d3..5462ae1 100644 --- a/fuzzycat/grobid_unstructured.py +++ b/fuzzycat/grobid_unstructured.py @@ -18,6 +18,7 @@ from fatcat_openapi_client import ReleaseContrib, ReleaseEntity, ReleaseExtIds from fuzzycat.config import settings from fuzzycat.grobid2json import biblio_info +from fuzzycat.utils import clean_doi GROBID_API_BASE = settings.get("GROBID_API_BASE", "https://grobid.qa.fatcat.wiki") @@ -89,7 +90,7 @@ def grobid_ref_to_release(ref: dict) -> ReleaseEntity: issue=ref.get("issue"), pages=ref.get("pages"), ext_ids=ReleaseExtIds( - doi=ref.get("doi"), + doi=clean_doi(ref.get("doi")), pmid=ref.get("pmid"), pmcid=ref.get("pmcid"), arxiv=ref.get("arxiv_id"), diff --git a/fuzzycat/simple.py b/fuzzycat/simple.py index c78ac28..8b206b1 100644 --- a/fuzzycat/simple.py +++ b/fuzzycat/simple.py @@ -26,6 +26,7 @@ from fuzzycat.entities import entity_to_dict from fuzzycat.grobid_unstructured import grobid_parse_unstructured from fuzzycat.matching import match_release_fuzzy from fuzzycat.verify import verify +from fuzzycat.utils import clean_doi @dataclass @@ -184,7 +185,7 @@ def biblio_to_release(biblio: dict) -> ReleaseEntity: release = ReleaseEntity( title=biblio.get("title"), ext_ids=ReleaseExtIds( - doi=biblio.get("doi"), + doi=clean_doi(biblio.get("doi")), pmid=biblio.get("pmid"), pmcid=biblio.get("pmcid"), arxiv=biblio.get("arxiv_id"), diff --git a/fuzzycat/utils.py b/fuzzycat/utils.py index bdca7b6..a1c5124 100644 --- a/fuzzycat/utils.py +++ b/fuzzycat/utils.py @@ -6,6 +6,7 @@ import re import string import subprocess import tempfile +from typing import Optional import requests from glom import PathAccessError, glom @@ -80,6 +81,19 @@ def dict_key_exists(doc, path): else: return True +def clean_doi(raw: Optional[str]) -> Optional[str]: + if not raw: + return None + raw = raw.strip().lower() + if raw.startswith("doi:"): + raw = raw[4:] + 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:] + return raw def doi_prefix(v): """ diff --git a/fuzzycat/verify.py b/fuzzycat/verify.py index f32121d..1eeea40 100644 --- a/fuzzycat/verify.py +++ b/fuzzycat/verify.py @@ -92,7 +92,7 @@ from fuzzycat.data import (CONTAINER_NAME_BLACKLIST, PUBLISHER_BLACKLIST, TITLE_ from fuzzycat.entities import entity_to_dict from fuzzycat.utils import (author_similarity_score, contains_chemical_formula, dict_key_exists, doi_prefix, has_doi_prefix, jaccard, num_project, parse_page_string, - slugify_string) + slugify_string, clean_doi) Verify = collections.namedtuple("Verify", "status reason") @@ -167,8 +167,8 @@ def verify(a: Dict, b: Dict, min_title_length=5) -> Tuple[str, str]: # A few items have the same DOI. try: - a_doi = glom(a, "ext_ids.doi") - b_doi = glom(b, "ext_ids.doi") + a_doi = clean_doi(glom(a, "ext_ids.doi")) + b_doi = clean_doi(glom(b, "ext_ids.doi")) if a_doi is not None and a_doi == b_doi: return Verify(Status.EXACT, Reason.DOI) except PathAccessError: diff --git a/tests/test_utils.py b/tests/test_utils.py index d0bcfc1..21b85a4 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -3,7 +3,7 @@ import os from fuzzycat.utils import (author_similarity_score, cut, jaccard, nwise, slugify_string, token_n_grams, tokenize_string, parse_page_string, dict_key_exists, - zstdlines, es_compat_hits_total) + zstdlines, es_compat_hits_total, clean_doi) def test_slugify_string(): @@ -123,3 +123,16 @@ def test_es_compat_hits_total(): ) for r, expected in cases: assert es_compat_hits_total(r) == expected + +def test_clean_doi(): + assert clean_doi(None) == None + assert clean_doi("blah") == None + 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("http://doi.org/10.1234/asdf ") == "10.1234/asdf" + # GROBID mangled DOI + assert clean_doi("21924DOI10.1234/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("10.7326/M20-6817") == "10.7326/m20-6817" |