rip out API interaction code

2 files changed, 3 insertions, 159 deletions

diff --git a/grobid_tei_xml/grobid_unstructured.py b/grobid_tei_xml/grobid_unstructured.py
index 5462ae1..83808e0 100644
--- a/grobid_tei_xml/grobid_unstructured.py
+++ b/grobid_tei_xml/grobid_unstructured.py
@@ -13,46 +13,7 @@ import sys
 import xml.etree.ElementTree as ET
 from typing import Optional
 
-import requests
-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")
-
-
-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
+from .grobid2json import biblio_info
 
 
 def transform_grobid_ref_xml(raw_xml: str) -> Optional[dict]:
@@ -60,7 +21,7 @@ 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
+    # first, remove any xmlns stuff, for consistent parsing
     raw_xml = raw_xml.replace('xmlns="http://www.tei-c.org/ns/1.0"', "")
     tree = ET.parse(io.StringIO(raw_xml))
     root = tree.getroot()
@@ -69,59 +30,3 @@ def transform_grobid_ref_xml(raw_xml: str) -> Optional[dict]:
         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=clean_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)
diff --git a/tests/test_grobid_unstructured.py b/tests/test_grobid_unstructured.py
index dd69936..b8d79ca 100644
--- a/tests/test_grobid_unstructured.py
+++ b/tests/test_grobid_unstructured.py
@@ -1,36 +1,6 @@
 import pytest
 
-from fuzzycat.grobid_unstructured import grobid_api_process_citation, grobid_parse_unstructured, grobid_ref_to_release, transform_grobid_ref_xml
-
-
-def test_grobid_ref_to_release():
-
-    d = {
-        'title':
-        "some title",
-        'doi':
-        '10.1234/5678',
-        'journal':
-        'some journal',
-        'authors': [
-            {
-                'name': 'ahab sailor',
-                'given_name': 'ahab',
-                'surname': 'sailor'
-            },
-            {
-                'name': 'mary jane',
-                'given_name': 'mary',
-                'surname': 'jane'
-            },
-        ],
-    }
-    r = grobid_ref_to_release(d)
-    assert r.title == d['title']
-    assert r.ext_ids.doi == d['doi']
-    assert r.extra['container_name'] == d['journal']
-    assert r.contribs[0].surname == d['authors'][0]['surname']
-    assert r.contribs[1].raw_name == d['authors'][1]['name']
+from grobid_tei_xml.grobid_unstructured import transform_grobid_ref_xml
 
 
 def test_transform_grobid_ref_xml():
@@ -97,34 +67,3 @@ def test_transform_grobid_ref_xml():
     assert d['journal'] == "Hernia"
 
 
-def test_grobid_parse_unstructured():
-    """
-    NOTE: this test makes live network requests to GROBID
-    """
-
-    r = grobid_parse_unstructured("blah")
-    assert r is None
-
-    r = grobid_parse_unstructured(
-        """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."""
-    )
-    assert r.title == "Mesh migration following abdominal hernia repair: a comprehensive review"
-    assert r.contribs[0].surname == "Cunningham"
-    assert r.contribs[1].surname == "Weis"
-    assert r.contribs[2].surname == "Taveras"
-    assert r.contribs[3].surname == "Huerta"
-    assert r.extra['container_name'] == "Hernia"
-    assert r.release_year == 2019
-    assert r.volume == "23"
-    assert r.issue == "2"
-    assert r.pages == "235-243"
-    assert r.ext_ids.doi == "10.1007/s10029-019-01898-9"
-    assert r.ext_ids.pmid == "30701369"
-
-
-def test_grobid_parse_unstructured_timeout():
-    """
-    NOTE: this test makes live network requests to GROBID
-    """
-    with pytest.raises(TimeoutError):
-        grobid_parse_unstructured("blah", timeout=0.000001)