GROBID API unstructured citation parsing utility code

2 files changed, 128 insertions, 1 deletions

diff --git a/fuzzycat/grobid2json.py b/fuzzycat/grobid2json.py
index 49f265a..c5aa0d2 100755
--- a/fuzzycat/grobid2json.py
+++ b/fuzzycat/grobid2json.py
@@ -26,7 +26,8 @@ def all_authors(elem: Optional[ET.Element], ns: str = ns) -> List[Dict[str, Any]
             continue
         given_name = pn.findtext("./{%s}forename" % ns) or None
         surname = pn.findtext("./{%s}surname" % ns) or None
-        full_name = " ".join(pn.itertext())
+        full_name = " ".join(pn.itertext()).strip()
+        full_name = " ".join(full_name.split())
         obj: Dict[str, Any] = dict(name=full_name)
         if given_name:
             obj["given_name"] = given_name
diff --git a/fuzzycat/grobid_unstructured.py b/fuzzycat/grobid_unstructured.py
new file mode 100644
index 0000000..4f09bce
--- /dev/null
+++ b/fuzzycat/grobid_unstructured.py
@@ -0,0 +1,126 @@
+"""
+Helper functions to parse an unstructured citation string using GROBID, then
+fuzzy match using the result.
+
+- try to parse string with GROBID REST API call
+- transform the GROBID XML response to a simple dict/struct
+
+TODO: more general versions which handle multiple reference strings in a batch?
+"""
+
+import io
+import sys
+import xml.etree.ElementTree as ET
+from typing import Any, Optional, Tuple
+
+import requests
+from fatcat_openapi_client import ReleaseContrib, ReleaseEntity, ReleaseExtIds
+
+from fuzzycat.config import settings
+from fuzzycat.grobid2json import biblio_info
+
+GROBID_API_BASE = settings.get("GROBID_API_BASE", "https://grobid.qa.fatcat.wiki")
+
+
+def grobid_api_process_citation(raw_citation: str,
+                                grobid_api_base: str = GROBID_API_BASE,
+                                timeout: float = 20.0) -> Optional[str]:
+    """
+    Process a single citation string using GROBID API, returning a TEI-XML response.
+
+    Raises python TimeoutError if there was a network or request timeout.
+
+    Raises a 'requests' error other unexpected failures (including network
+    connection failures)
+    """
+    try:
+        grobid_response = requests.post(
+            grobid_api_base + "/api/processCitation",
+            data={
+                "citations": raw_citation,
+                "consolidateCitations": 0,
+            },
+            timeout=timeout,
+        )
+    except requests.Timeout:
+        raise TimeoutError("GROBID request (HTTP POST) timeout")
+
+    if grobid_response.status_code == 204:
+        return None
+    elif grobid_response.status_code != 200:
+        print(f"GROBID request (HTTP POST) failed: {grobid_response}", file=sys.stderr)
+    grobid_response.raise_for_status()
+
+    return grobid_response.text or None
+
+
+def transform_grobid_ref_xml(raw_xml: str) -> Optional[dict]:
+    """
+    Parses GROBID XML for the case of a single reference/citation string (eg,
+    not a full/propper TEI-XML fulltext document), and returns a dict.
+    """
+    # first, remove any xmlns stuff, for consistent parsign
+    raw_xml = raw_xml.replace('xmlns="http://www.tei-c.org/ns/1.0"', "")
+    tree = ET.parse(io.StringIO(raw_xml))
+    root = tree.getroot()
+    ref = biblio_info(root, ns="")
+    if not any(ref.values()):
+        return None
+    return ref
+
+
+def grobid_ref_to_release(ref: dict) -> ReleaseEntity:
+    """
+    Takes the dict returned by transform_grobid_ref_xml() and returns a partial
+    ReleaseEntity object (for use with fuzzycat)
+    """
+    contribs = []
+    for author in ref.get("authors") or []:
+        contribs.append(
+            ReleaseContrib(
+                raw_name=author.get("name"),
+                given_name=author.get("given_name"),
+                surname=author.get("surname"),
+            ))
+    release = ReleaseEntity(
+        title=ref.get("title"),
+        contribs=contribs,
+        volume=ref.get("volume"),
+        issue=ref.get("issue"),
+        pages=ref.get("pages"),
+        ext_ids=ReleaseExtIds(
+            doi=ref.get("doi"),
+            pmid=ref.get("pmid"),
+            pmcid=ref.get("pmcid"),
+            arxiv=ref.get("arxiv_id"),
+        ),
+    )
+    if ref.get("journal"):
+        release.extra = {"container_name": ref.get("journal")}
+    if ref.get("date"):
+        if len(ref["date"]) >= 4 and ref["date"][0:4].isdigit():
+            release.release_year = int(ref["date"][0:4])
+        # TODO: try to parse 'date' into an ISO date format, and assign to release_date?
+    return release
+
+
+def grobid_parse_unstructured(raw_citation: str,
+                              grobid_api_base: str = GROBID_API_BASE,
+                              timeout: float = 20.0) -> Optional[ReleaseEntity]:
+    """
+    High-level wrapper to parse a raw citation string into a (partial) release
+    entity.
+    
+    Returns None if it fails to parse.
+
+    Raises various exceptions on network or remote errors.
+    """
+    ref_xml = grobid_api_process_citation(raw_citation,
+                                          grobid_api_base=grobid_api_base,
+                                          timeout=timeout)
+    if not ref_xml:
+        return None
+    biblio_dict = transform_grobid_ref_xml(ref_xml)
+    if not biblio_dict:
+        return None
+    return grobid_ref_to_release(biblio_dict)