add 'simple' high-level routines for fuzzy-match-and-verify calls

Some of these are a little redundant, in that calling code could
trivially re-implement. However, I think these are good starters for
stable external API interfaces, leaving us room to iterate and refactor
lower-level implementations behind the scenes.

2 files changed, 316 insertions, 0 deletions

diff --git a/fuzzycat/simple.py b/fuzzycat/simple.py
new file mode 100644
index 0000000..c78ac28
--- /dev/null
+++ b/fuzzycat/simple.py
@@ -0,0 +1,274 @@
+"""
+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
diff --git a/tests/test_simple.py b/tests/test_simple.py
new file mode 100644
index 0000000..0c5d216
--- /dev/null
+++ b/tests/test_simple.py
@@ -0,0 +1,42 @@
+"""
+These basically all hit external network services.
+"""
+
+import pytest
+import elasticsearch
+
+from fuzzycat.simple import *
+from fuzzycat.config import settings
+
+
+@pytest.fixture
+def es_client():
+    return elasticsearch.Elasticsearch(
+        [settings.get("FATCAT_SEARCH_URL", "https://search.fatcat.wiki:443")])
+
+
+def test_close_fuzzy_unstructured_matches(es_client):
+
+    matches = close_fuzzy_unstructured_matches(
+        """Cunningham HB, Weis JJ, Taveras LR, Huerta S. Mesh migration following abdominal hernia repair: a comprehensive review. Hernia. 2019 Apr;23(2):235-243. doi: 10.1007/s10029-019-01898-9. Epub 2019 Jan 30. PMID: 30701369.""",
+        es_client=es_client)
+
+    assert matches
+    assert matches[0].status.name == "EXACT"
+    assert matches[0].release.ext_ids.doi == "10.1007/s10029-019-01898-9"
+
+
+def test_close_fuzzy_biblio_matches(es_client):
+
+    matches = close_fuzzy_biblio_matches(dict(
+        title="Mesh migration following abdominal hernia repair: a comprehensive review",
+        first_author="Cunningham",
+        year=2019,
+        journal="Hernia",
+    ),
+                                         es_client=es_client)
+
+    assert matches
+    # TODO: should be "STRONG" or "WEAK" without all authors?
+    assert matches[0].status.name in ("STRONG", "WEAK", "AMBIGUOUS")
+    assert matches[0].release.ext_ids.doi == "10.1007/s10029-019-01898-9"