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"""
This file contains simple high-level functions that call in to match, verify,
and unstructured parsing routines.
close_fuzzy_release_matches(release) -> List[FuzzyReleaseMatchResult]
close_fuzzy_biblio_matches(biblio) -> List[FuzzyReleaseMatchResult]
close_fuzzy_unstructured_matches(unstructured) -> List[FuzzyReleaseMatchResult]
Each function takes additional arguments:
es_client
fatcat_api_client
match_limit
Each also has a "closest" variant, which returns just the single highest-rated
match.
"""
from dataclasses import dataclass
from typing import Any, List, Optional
from fatcat_openapi_client import ReleaseContrib, ReleaseEntity, ReleaseExtIds
from fuzzycat.common import Reason, Status
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
@dataclass
class FuzzyReleaseMatchResult:
status: Status
reason: Reason
release: ReleaseEntity
# this map used to establish priority order of verified matches
STATUS_SORT = {
Status.TODO: 0,
Status.EXACT: 10,
Status.STRONG: 20,
Status.WEAK: 30,
Status.AMBIGUOUS: 40,
Status.DIFFERENT: 60,
}
def close_fuzzy_release_matches(release: ReleaseEntity,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> Optional[FuzzyReleaseMatchResult]:
"""
This high-level helper function runs a fuzzy match (using elasticsearch),
verifies all the results, and returns the "closest" matching results (if
any).
es_client is required, and used in the matcing process.
fatcat_api_client is optional and used both for entity-to-dict conversion
efficiency and for fetching current entities from the fatcat API
match_limit sets the maximum result size from the inital fuzzy match call
Returns an empty list if there was no match of any kind, or a sorted list
of simple result objects (FuzzyReleaseMatchResult dataclass) with fields:
status: fuzzycat.common.Status
reason: fuzzycat.common.Reason
release: ReleaseEntity
Status is one of the fuzzycat.common.Status, with "strongest match" in this
sorted order:
- EXACT
- STRONG
- WEAK
- AMBIGUOUS
DIFFERENT and TODO matches are never returned.
Eg, if there is any EXACT match that is always returned; an AMBIGIOUS
result is only returned if all the candidate matches were ambiguous.
"""
candidates = match_release_fuzzy(release, size=match_limit, es=es_client)
if not candidates:
return None
release_dict = entity_to_dict(release, api_client=fatcat_api_client)
# list of tuple of (Verify, ReleaseEntity)
verified = [(
verify(release_dict, entity_to_dict(c, api_client=fatcat_api_client)),
c,
) for c in candidates]
# list of FuzzyReleaseMatchResult, with TODO and DIFFERENT removed
verified = [
FuzzyReleaseMatchResult(v[0].status, v[0].reason, v[1]) for v in verified
if v[0].status not in [Status.TODO, Status.DIFFERENT]
]
return sorted(verified, key=lambda v: STATUS_SORT[v.status])
def closest_fuzzy_release_match(release: ReleaseEntity,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> Optional[FuzzyReleaseMatchResult]:
"""
Single-result variant of close_fuzzy_release_matches()
"""
matches = close_fuzzy_release_matches(
release,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
if matches:
return matches[0]
else:
return None
def close_fuzzy_unstructured_matches(raw_citation: str,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Variation of close_fuzzy_release_matches() which first parses an
unstructured citation string, then finds close matches.
TODO: pass-through GROBID API configuration?
"""
release = grobid_parse_unstructured(raw_citation)
if not release:
return None
return close_fuzzy_release_matches(
release,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
def closest_fuzzy_unstructured_match(raw_citation: str,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Single-result variant of close_fuzzy_release_matches()
"""
matches = close_fuzzy_unstructured_matches(
raw_citation,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
if matches:
return matches[0]
else:
return None
def biblio_to_release(biblio: dict) -> ReleaseEntity:
"""
Helper for close_fuzzy_biblio_matches() et al
"""
contribs = []
if biblio.get('authors'):
for a in biblio['authors']:
contribs.append(
ReleaseContrib(
raw_name=a.get('name'),
given_name=a.get('given_name'),
surname=a.get('surname'),
))
elif biblio.get('author_names'):
for a in biblio['author_names']:
contribs.append(ReleaseContrib(raw_name=a))
elif biblio.get('first_author'):
contribs.append(ReleaseContrib(raw_name=biblio['first_author']))
release = ReleaseEntity(
title=biblio.get("title"),
ext_ids=ReleaseExtIds(
doi=biblio.get("doi"),
pmid=biblio.get("pmid"),
pmcid=biblio.get("pmcid"),
arxiv=biblio.get("arxiv_id"),
),
volume=biblio.get("volume"),
issue=biblio.get("issue"),
pages=biblio.get("pages") or biblio.get("first_page"),
publisher=biblio.get("publisher"),
release_stage=biblio.get("release_stage"),
release_type=biblio.get("release_type"),
extra=dict(),
)
if biblio.get('journal'):
release.extra['container_name'] = biblio['journal']
elif biblio.get('conference'):
release.extra['container_name'] = biblio['conference']
if biblio.get('year'):
year = biblio['year']
if isinstance(year, str) and len(year) >= 4 and year[0:4].isdigit():
release.release_year = int(year[0:4])
elif isinstance(year, int):
release.release_year = year
elif biblio.get('date'):
date = biblio['date']
if isinstance(date, str) and len(date) >= 4 and date[0:4].isdigit():
release.release_year = int(date[0:4])
return release
def close_fuzzy_biblio_matches(biblio: dict,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Variation of close_fuzzy_release_matches() which takes bibliographic fields
as arguments.
Biblio fields which are handled include:
title
journal
or: conference
authors
name
given_name
surname
or: author_names (List[str])
or: first_author (str)
year
date
volume
issue
pages
or: first_page
publisher
doi
pmid
arxiv_id
release_type (eg, 'journal-article', 'book', 'dataset')
release_stage
"""
release = biblio_to_release(biblio)
return close_fuzzy_release_matches(
release,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
def closest_fuzzy_biblio_match(biblio: dict,
es_client: Any,
fatcat_api_client: Optional[Any] = None,
match_limit: int = 5) -> List[FuzzyReleaseMatchResult]:
"""
Single-result variant of close_fuzzy_biblio_matches()
"""
matches = close_fuzzy_biblio_matches(
biblio,
es_client=es_client,
fatcat_api_client=fatcat_api_client,
match_limit=match_limit,
)
if matches:
return matches[0]
else:
return None
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