Merge branch 'bnewbold-refs-apis'

1 files changed, 429 insertions, 0 deletions

diff --git a/python/fatcat_tools/references.py b/python/fatcat_tools/references.py
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+"""
+Helper routines for working with the fatcat citation graph, which is a separate
+index of reference links between works in the main catalog.
+
+See bulk citation and citation API proposals for design documentation.
+"""
+
+import sys
+import datetime
+import argparse
+from typing import Optional, List, Any, Dict, Union
+
+from pydantic import BaseModel, validator
+import elasticsearch
+from elasticsearch_dsl import Search
+from fatcat_openapi_client import ReleaseEntity
+
+from fatcat_tools import public_api
+from fatcat_tools.transforms.access import release_access_options, AccessOption
+from fatcat_tools.transforms.entities import entity_to_dict
+
+
+class BiblioRef(BaseModel):
+    """bibliographic reference"""
+    # ("release", source_release_ident, ref_index)
+    # ("wikipedia", source_wikipedia_article, ref_index)
+    _key: Optional[str]
+    update_ts: Optional[datetime.datetime]
+
+    # metadata about source of reference
+    source_release_ident: Optional[str]
+    source_work_ident: Optional[str]
+    # with lang prefix like "en:Superglue"
+    source_wikipedia_article: Optional[str]
+    source_release_stage: Optional[str]
+    source_year: Optional[int]
+
+    # context of the reference itself
+    # 1-indexed, not 0-indexed
+    ref_index: Optional[int] # TODO: actually optional?
+    # eg, "Lee86", "BIB23"
+    ref_key: Optional[str]
+    # eg, page number
+    ref_locator: Optional[str]
+
+    # target of reference (identifiers)
+    target_release_ident: Optional[str]
+    target_work_ident: Optional[str]
+    target_openlibrary_work: Optional[str]
+    # TODO: target_url_surt: Optional[str]
+    # would not be stored in elasticsearch, but would be auto-generated by all "get" methods from the SURT, so calling code does not need to do SURT transform
+    target_url: Optional[str]
+
+    # crossref, pubmed, grobid, etc
+    match_provenance: Optional[str]
+    # strong, weak, etc
+    match_status: Optional[str]
+    # TODO: "match_strength"?
+    # "doi", "isbn", "fuzzy title, author", etc
+    # maybe "fuzzy-title-author"?
+    match_reason: Optional[str]
+
+    # only if no release_ident link/match
+    target_unstructured: Optional[str]
+    target_csl: Optional[Dict[str, Any]]
+
+    def hacks(self):
+        """
+        Temporary (?) hacks to work around schema/data issues
+        """
+        if self.target_openlibrary_work and self.target_openlibrary_work.startswith("/works/"):
+            self.target_openlibrary_work = self.target_openlibrary_work[7:]
+
+        # work-arounds for bad/weird ref_key
+        if self.ref_key:
+            self.ref_key = self.ref_key.strip()
+            if self.ref_key[0] in ['/', '_']:
+                self.ref_key = self.ref_key[1:]
+            if self.ref_key.startswith("10.") and 'SICI' in self.ref_key and '-' in self.ref_key:
+                self.ref_key = self.ref_key.split('-')[-1]
+            if self.ref_key.startswith("10.") and '_' in self.ref_key:
+                self.ref_key = self.ref_key.split('_')[-1]
+            if len(self.ref_key) > 10 and "#" in self.ref_key:
+                self.ref_key = self.ref_key.split('#')[-1]
+            if len(self.ref_key) > 10 and "_" in self.ref_key:
+                self.ref_key = self.ref_key.split('_')[-1]
+        if not self.ref_key and self.ref_index is not None:
+            self.ref_key = str(self.ref_index)
+        return self
+
+
+class EnrichedBiblioRef(BaseModel):
+    # enriched version of BiblioRef with complete ReleaseEntity object as
+    # fetched from the fatcat API. CSL-JSON metadata would be derived from
+    # the full release entity.
+    ref: BiblioRef
+    release: Optional[ReleaseEntity]
+    # TODO: openlibrary work?
+    access: List[AccessOption]
+
+    @validator('release')
+    @classmethod
+    def check_release(cls, v):
+        if v is not None and not isinstance(v, ReleaseEntity):
+            raise ValueError("expected a ReleaseEntity")
+        return v
+
+    class Config:
+        arbitrary_types_allowed = True
+        json_encoders = {
+            ReleaseEntity: entity_to_dict,
+        }
+
+
+class RefHits(BaseModel):
+    count_returned: int
+    count_total: int
+    offset: int
+    limit: int
+    query_time_ms: int
+    query_wall_time_ms: int
+    result_refs: List[Union[BiblioRef,EnrichedBiblioRef]]
+
+    class Config:
+        json_encoders = {
+            ReleaseEntity: entity_to_dict,
+        }
+
+
+def _execute_ref_query(search: Any, limit: int, offset: Optional[int] = None) -> RefHits:
+    """
+    Internal helper for querying elasticsearch refs index and transforming hits
+    """
+
+    limit = min((int(limit or 15), 200))
+    if not offset or offset < 0:
+        offset = 0
+
+    search = search.params(track_total_hits=True)
+    search = search[offset : (offset + limit)]
+
+    query_start = datetime.datetime.now()
+    try:
+        resp = search.execute()
+    except elasticsearch.exceptions.RequestError as e_raw:
+        # this is a "user" error
+        e: Any = e_raw
+        #logging.warn("elasticsearch 400: " + str(e.info))
+        if e.info.get("error", {}).get("root_cause", {}):
+            raise ValueError(str(e.info["error"]["root_cause"][0].get("reason"))) from e
+        else:
+            raise ValueError(str(e.info)) from e
+    except elasticsearch.exceptions.TransportError as e:
+        # all other errors
+        #logging.warn(f"elasticsearch non-200 status code: {e.info}")
+        raise IOError(str(e.info)) from e
+    query_delta = datetime.datetime.now() - query_start
+
+    result_refs = []
+    for h in resp.hits:
+        # might be a list because of consolidation
+        if isinstance(h._d_.get('source_work_ident'), list):
+            h._d_['source_work_ident'] = h._d_['source_work_ident'][0]
+        result_refs.append(BiblioRef.parse_obj(h._d_).hacks())
+
+    return RefHits(
+        count_returned=len(result_refs),
+        # ES 7.x style "total"
+        count_total=resp.hits.total.value,
+        offset=offset,
+        limit=limit,
+        query_time_ms=int(resp.took),
+        query_wall_time_ms=int(query_delta.total_seconds() * 1000),
+        result_refs=result_refs,
+    )
+
+
+def get_outbound_refs(
+    es_client: Any,
+    release_ident: Optional[str] = None,
+    work_ident: Optional[str] = None,
+    wikipedia_article: Optional[str] = None,
+    limit: int = 100,
+    offset: Optional[int] = None,
+    es_index: str = "fatcat_ref",
+) -> RefHits:
+
+    search = Search(using=es_client, index=es_index)
+
+    if release_ident:
+        search = search.filter("term", source_release_ident=release_ident)
+    elif work_ident:
+        search = search.filter("term", source_work_ident=work_ident)
+    elif wikipedia_article:
+        search = search.filter("term", source_wikipedia_article=wikipedia_article)
+    else:
+        raise ValueError("require a lookup key")
+
+    search = search.sort("ref_index")
+
+    # re-sort by index
+    hits = _execute_ref_query(search, limit=limit, offset=offset)
+    hits.result_refs = sorted(hits.result_refs, key=lambda r: r.ref_index or 0)
+    return hits
+
+
+def get_inbound_refs(
+    es_client: Any,
+    release_ident: Optional[str] = None,
+    work_ident: Optional[str] = None,
+    openlibrary_work: Optional[str] = None,
+    url: Optional[str] = None,
+    consolidate_works: bool = True,
+    filter_stage: List[str] = [],
+    sort: Optional[str] = None,
+    limit: int = 25,
+    offset: Optional[int] = None,
+    es_index: str = "fatcat_ref",
+) -> List[BiblioRef]:
+
+    search = Search(using=es_client, index=es_index)
+
+    if consolidate_works:
+        search = search.extra(
+            collapse={
+                "field": "source_work_ident",
+                "inner_hits": {"name": "source_more", "size": 0,},
+            }
+        )
+
+    if release_ident:
+        search = search.filter("term", target_release_ident=release_ident)
+    elif work_ident:
+        search = search.filter("term", target_work_ident=work_ident)
+    elif openlibrary_work:
+        search = search.filter("term", target_openlibrary_work=openlibrary_work)
+    else:
+        raise ValueError("require a lookup key")
+
+    if filter_stage:
+        search = search.filter("term", source_stage=filter_stage)
+
+    if sort == "newest":
+        search = search.sort("-source_year")
+    elif sort == "oldest":
+        search = search.sort("source_year")
+    else:
+        search = search.sort("-source_year")
+
+    return _execute_ref_query(search, limit=limit, offset=offset)
+
+
+def count_inbound_refs(
+    es_client: Any,
+    release_ident: Optional[str] = None,
+    work_ident: Optional[str] = None,
+    openlibrary_work: Optional[str] = None,
+    url: Optional[str] = None,
+    filter_stage: List[str] = [],
+    es_index: str = "fatcat_ref",
+) -> int:
+    """
+    Same parameters as get_inbound_refs(), but returns just a count
+    """
+
+    search = Search(using=es_client, index=es_index)
+
+    if release_ident:
+        search = search.filter("term", target_release_ident=release_ident)
+    elif work_ident:
+        search = search.filter("term", target_work_ident=work_ident)
+    elif openlibrary_work:
+        search = search.filter("term", target_openlibrary_work=openlibrary_work)
+    else:
+        raise ValueError("require a lookup key")
+
+    if filter_stage:
+        search = search.filter("term", source_stage=filter_stage)
+
+    return search.count()
+
+
+# run fatcat API fetches for each ref and return "enriched" refs
+def enrich_inbound_refs(refs: List[BiblioRef], fatcat_api_client: Any, hide: Optional[str] = "refs", expand: Optional[str] = "container,files,webcaptures,filesets") -> List[EnrichedBiblioRef]:
+    enriched = []
+    for ref in refs:
+        release = None
+        access = []
+        if ref.source_release_ident:
+            release = fatcat_api_client.get_release(ref.source_release_ident, hide=hide, expand=expand)
+            access = release_access_options(release)
+        if ref.source_wikipedia_article:
+            wiki_lang = ref.source_wikipedia_article.split(':')[0]
+            wiki_article = ':'.join(ref.source_wikipedia_article.split(':')[1:]).replace(' ', '_')
+            access.append(AccessOption(
+                access_type="wikipedia",
+                access_url=f"https://{wiki_lang}.wikipedia.org/wiki/{wiki_article}",
+                mimetype=None,
+                size_bytes=None,
+                thumbnail_url=None
+            ))
+        enriched.append(EnrichedBiblioRef(
+            ref=ref,
+            access=access,
+            release=release,
+        ))
+    return enriched
+
+
+def enrich_outbound_refs(refs: List[BiblioRef], fatcat_api_client: Any, hide: Optional[str] = "refs", expand: Optional[str] = "container,files,webcaptures,filesets") -> List[EnrichedBiblioRef]:
+    enriched = []
+    for ref in refs:
+        release = None
+        access = []
+        if ref.target_release_ident:
+            release = fatcat_api_client.get_release(ref.target_release_ident, hide=hide, expand=expand)
+            access = release_access_options(release)
+        if ref.target_openlibrary_work:
+            access.append(AccessOption(
+                access_type="openlibrary",
+                access_url=f"https://openlibrary.org/works/{ref.target_openlibrary_work}",
+                mimetype=None,
+                size_bytes=None,
+                thumbnail_url=None
+            ))
+        if ref.target_url and '://web.archive.org/' in ref.target_url:
+            access.append(AccessOption(
+                access_type="wayback",
+                access_url=ref.target_url,
+                mimetype=None,
+                size_bytes=None,
+                thumbnail_url=None
+            ))
+        enriched.append(EnrichedBiblioRef(
+            ref=ref,
+            access=access,
+            release=release,
+        ))
+    return enriched
+
+
+def run_ref_query(args) -> None:
+    """
+    CLI helper/debug tool (prints to stdout)
+    """
+    release_ident = None
+    work_ident = None
+    if args.ident.startswith("release_"):
+        release_ident = args.ident.split('_')[1]
+    elif args.ident.startswith("work_"):
+        work_ident = args.ident.split('_')[1]
+    else:
+        release_ident = args.ident
+
+    print("## Outbound References")
+    hits = get_outbound_refs(release_ident=release_ident, work_ident=work_ident, es_client=args.es_client)
+    print(f"Total: {hits.count_total}  Time: {hits.query_wall_time_ms}ms; {hits.query_time_ms}ms")
+
+    if args.enrich == "fatcat":
+        enriched = enrich_outbound_refs(hits.result_refs, hide='refs,abstracts', fatcat_api_client=args.fatcat_api_client)
+        for ref in enriched:
+            if ref.release:
+                print(f"{ref.ref.ref_index or '-'}\trelease_{ref.release.ident}\t{ref.ref.match_provenance}/{ref.ref.match_status}\t{ref.release.release_year or '-'}\t{ref.release.title}\t{ref.release.ext_ids.pmid or ref.release.ext_ids.doi or '-'}")
+            else:
+                print(f"{ref.ref.ref_index or '-'}\trelease_{ref.target_release_ident}")
+    else:
+        for ref in hits.result_refs:
+            print(f"{ref.ref.ref_index or '-'}\trelease_{ref.target_release_ident}")
+
+    print()
+    print("## Inbound References")
+    hits = get_inbound_refs(release_ident=release_ident, work_ident=work_ident, es_client=args.es_client)
+
+    print(f"Total: {hits.count_total}  Time: {hits.query_wall_time_ms}ms; {hits.query_time_ms}ms")
+
+    if args.enrich == "fatcat":
+        enriched = enrich_inbound_refs(hits.result_refs, hide='refs,abstracts', fatcat_api_client=args.fatcat_api_client)
+        for ref in enriched:
+            if ref.release:
+                print(f"release_{ref.release.ident}\t{ref.ref.match_provenance}/{ref.ref.match_status}\t{ref.release.release_year or '-'}\t{ref.release.title}\t{ref.release.ext_ids.pmid or ref.release.ext_ids.doi or '-'}")
+            else:
+                print(f"release_{ref.target_release_ident}")
+    else:
+        for ref in hits.result_refs:
+            print(f"work_{ref.source_work_ident}\trelease_{ref.source_release_ident}")
+
+def main() -> None:
+    """
+    Run this utility like:
+
+        python -m fatcat_tools.references
+
+    Examples:
+
+        python -m fatcat_tools.references query release_pfrind3kh5hqhgqkueulk2tply
+    """
+
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    subparsers = parser.add_subparsers()
+
+    parser.add_argument("--fatcat-api-base", default="https://api.fatcat.wiki/v0")
+    parser.add_argument("--elasticsearch-base", default="https://search.fatcat.wiki")
+    parser.add_argument("--elasticsearch-ref-index", default="fatcat_ref")
+
+    sub = subparsers.add_parser(
+        "query",
+        help="takes a fatcat ident argument, prints both inbound and outbound references",
+    )
+    sub.set_defaults(func="run_ref_query")
+    sub.add_argument("ident", type=str)
+    sub.add_argument("--enrich", type=str)
+
+    args = parser.parse_args()
+    if not args.__dict__.get("func"):
+        parser.print_help(file=sys.stderr)
+        sys.exit(-1)
+
+    args.es_client = elasticsearch.Elasticsearch(args.elasticsearch_base)
+    args.fatcat_api_client = public_api(args.fatcat_api_base)
+
+    if args.func == "run_ref_query":
+        run_ref_query(args)
+    else:
+        raise NotImplementedError(args.func)
+
+if __name__ == "__main__":
+    main()