make fmt

4 files changed, 39 insertions, 31 deletions

diff --git a/grobid_tei_xml/grobid2json.py b/grobid_tei_xml/grobid2json.py
index ac0710c..5edee36 100755
--- a/grobid_tei_xml/grobid2json.py
+++ b/grobid_tei_xml/grobid2json.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-
 """
 NB: adapted to work as a library for PDF extraction. Will probably be
 re-written eventually to be correct, complete, and robust; this is just a
@@ -25,17 +24,18 @@ Prints JSON to stdout, errors to stderr
 This file copied from the sandcrawler repository.
 """
 
+import argparse
 import io
 import json
-import argparse
 import xml.etree.ElementTree as ET
-from typing import List, Any, Dict, AnyStr, Optional
+from typing import Any, AnyStr, Dict, List, Optional
 
 xml_ns = "http://www.w3.org/XML/1998/namespace"
 ns = "http://www.tei-c.org/ns/1.0"
 
 
-def all_authors(elem: Optional[ET.Element], ns: str = ns) -> List[Dict[str, Any]]:
+def all_authors(elem: Optional[ET.Element],
+                ns: str = ns) -> List[Dict[str, Any]]:
     if not elem:
         return []
     names = []
@@ -45,7 +45,8 @@ 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([t.strip() for t in pn.itertext() if t.strip()]).strip()
+        full_name = " ".join([t.strip() for t in pn.itertext()
+                              if t.strip()]).strip()
         obj: Dict[str, Any] = dict(name=full_name)
         if given_name:
             obj["given_name"] = given_name
@@ -79,8 +80,7 @@ def journal_info(elem: ET.Element) -> Dict[str, Any]:
     journal = dict()
     journal["name"] = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
     journal["publisher"] = elem.findtext(
-        f".//{{{ns}}}publicationStmt/{{{ns}}}publisher"
-    )
+        f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
     if journal["publisher"] == "":
         journal["publisher"] = None
     journal["issn"] = elem.findtext('.//{%s}idno[@type="ISSN"]' % ns)
@@ -99,7 +99,8 @@ def journal_info(elem: ET.Element) -> Dict[str, Any]:
 def biblio_info(elem: ET.Element, ns: str = ns) -> Dict[str, Any]:
     ref: Dict[str, Any] = dict()
     ref["id"] = elem.attrib.get("{http://www.w3.org/XML/1998/namespace}id")
-    ref["unstructured"] = elem.findtext('.//{%s}note[@type="raw_reference"]' % ns)
+    ref["unstructured"] = elem.findtext('.//{%s}note[@type="raw_reference"]' %
+                                        ns)
     # Title stuff is messy in references...
     ref["title"] = elem.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
     other_title = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
@@ -110,9 +111,11 @@ def biblio_info(elem: ET.Element, ns: str = ns) -> Dict[str, Any]:
             ref["journal"] = None
             ref["title"] = other_title
     ref["authors"] = all_authors(elem, ns=ns)
-    ref["publisher"] = elem.findtext(f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
+    ref["publisher"] = elem.findtext(
+        f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
     if not ref["publisher"]:
-        ref["publisher"] = elem.findtext(f".//{{{ns}}}imprint/{{{ns}}}publisher")
+        ref["publisher"] = elem.findtext(
+            f".//{{{ns}}}imprint/{{{ns}}}publisher")
     if ref["publisher"] == "":
         ref["publisher"] = None
     date = elem.find('.//{%s}date[@type="published"]' % ns)
@@ -162,23 +165,25 @@ def teixml2json(content: AnyStr, encumbered: bool = True) -> Dict[str, Any]:
     header = tei.find(".//{%s}teiHeader" % ns)
     if header is None:
         raise ValueError("XML does not look like TEI format")
-    application_tag = header.findall(f".//{{{ns}}}appInfo/{{{ns}}}application")[0]
+    application_tag = header.findall(
+        f".//{{{ns}}}appInfo/{{{ns}}}application")[0]
     info["grobid_version"] = application_tag.attrib["version"].strip()
     info["grobid_timestamp"] = application_tag.attrib["when"].strip()
     info["title"] = header.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
     info["authors"] = all_authors(
-        header.find(f".//{{{ns}}}sourceDesc/{{{ns}}}biblStruct")
-    )
+        header.find(f".//{{{ns}}}sourceDesc/{{{ns}}}biblStruct"))
     info["journal"] = journal_info(header)
     date = header.find('.//{%s}date[@type="published"]' % ns)
     info["date"] = (date is not None) and date.attrib.get("when")
-    info["fatcat_release"] = header.findtext('.//{%s}idno[@type="fatcat"]' % ns)
+    info["fatcat_release"] = header.findtext('.//{%s}idno[@type="fatcat"]' %
+                                             ns)
     info["doi"] = header.findtext('.//{%s}idno[@type="DOI"]' % ns)
     if info["doi"]:
         info["doi"] = info["doi"].lower()
 
     refs = []
-    for (i, bs) in enumerate(tei.findall(f".//{{{ns}}}listBibl/{{{ns}}}biblStruct")):
+    for (i, bs) in enumerate(
+            tei.findall(f".//{{{ns}}}listBibl/{{{ns}}}biblStruct")):
         ref = biblio_info(bs)
         ref["index"] = i
         refs.append(ref)
@@ -195,7 +200,8 @@ def teixml2json(content: AnyStr, encumbered: bool = True) -> Dict[str, Any]:
         el = tei.find(f".//{{{ns}}}text/{{{ns}}}body")
         info["body"] = (el or None) and " ".join(el.itertext()).strip()
         el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="acknowledgement"]')
-        info["acknowledgement"] = (el or None) and " ".join(el.itertext()).strip()
+        info["acknowledgement"] = (el or None) and " ".join(
+            el.itertext()).strip()
         el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="annex"]')
         info["annex"] = (el or None) and " ".join(el.itertext()).strip()
 
@@ -216,7 +222,8 @@ def main() -> None:  # pragma no cover
     parser.add_argument(
         "--no-encumbered",
         action="store_true",
-        help="don't include ambiguously copyright encumbered fields (eg, abstract, body)",
+        help=
+        "don't include ambiguously copyright encumbered fields (eg, abstract, body)",
     )
     parser.add_argument("teifiles", nargs="+")
 
@@ -228,8 +235,7 @@ def main() -> None:  # pragma no cover
             json.dumps(
                 teixml2json(content, encumbered=(not args.no_encumbered)),
                 sort_keys=True,
-            )
-        )
+            ))
 
 
 if __name__ == "__main__":  # pragma no cover
diff --git a/grobid_tei_xml/grobid_unstructured.py b/grobid_tei_xml/grobid_unstructured.py
index 83808e0..eeb3507 100644
--- a/grobid_tei_xml/grobid_unstructured.py
+++ b/grobid_tei_xml/grobid_unstructured.py
@@ -29,4 +29,3 @@ def transform_grobid_ref_xml(raw_xml: str) -> Optional[dict]:
     if not any(ref.values()):
         return None
     return ref
-
diff --git a/tests/test_grobid2json.py b/tests/test_grobid2json.py
index 7ee423c..6e3dac2 100644
--- a/tests/test_grobid2json.py
+++ b/tests/test_grobid2json.py
@@ -1,4 +1,3 @@
-
 import xml
 import json
 import pytest
@@ -6,14 +5,15 @@ from grobid_tei_xml.grobid2json import teixml2json
 
 
 def test_small_xml():
-    
+
     with open('tests/files/small.xml', 'r') as f:
         tei_xml = f.read()
     with open('tests/files/small.json', 'r') as f:
-        json_form  = json.loads(f.read())
+        json_form = json.loads(f.read())
 
     assert teixml2json(tei_xml) == json_form
 
+
 def test_invalid_xml():
 
     with pytest.raises(xml.etree.ElementTree.ParseError):
@@ -30,18 +30,22 @@ def test_grobid_teixml2json() -> None:
     obj = teixml2json(blob, True)
 
     assert (
-        obj["title"]
-        == "Changes of patients' satisfaction with the health care services in Lithuanian Health Promoting Hospitals network"
+        obj["title"] ==
+        "Changes of patients' satisfaction with the health care services in Lithuanian Health Promoting Hospitals network"
     )
 
     ref = [c for c in obj["citations"] if c["id"] == "b12"][0]
-    assert ref["authors"][0] == {"given_name": "K", "name": "K Tasa", "surname": "Tasa"}
+    assert ref["authors"][0] == {
+        "given_name": "K",
+        "name": "K Tasa",
+        "surname": "Tasa"
+    }
     assert ref["journal"] == "Quality Management in Health Care"
     assert ref["title"] == "Using patient feedback for quality improvement"
     assert ref["date"] == "1996"
     assert ref["pages"] == "206-225"
     assert ref["volume"] == "8"
     assert (
-        ref["unstructured"]
-        == "Tasa K, Baker R, Murray M. Using patient feedback for qua- lity improvement. Quality Management in Health Care 1996;8:206-19."
+        ref["unstructured"] ==
+        "Tasa K, Baker R, Murray M. Using patient feedback for qua- lity improvement. Quality Management in Health Care 1996;8:206-19."
     )
diff --git a/tests/test_grobid_unstructured.py b/tests/test_grobid_unstructured.py
index b8d79ca..b203b30 100644
--- a/tests/test_grobid_unstructured.py
+++ b/tests/test_grobid_unstructured.py
@@ -54,7 +54,8 @@ def test_transform_grobid_ref_xml():
 </biblStruct>"""
 
     d = transform_grobid_ref_xml(citation_xml)
-    assert d['title'] == "Mesh migration following abdominal hernia repair: a comprehensive review"
+    assert d[
+        'title'] == "Mesh migration following abdominal hernia repair: a comprehensive review"
     assert d['authors'][2]['given_name'] == "L"
     assert d['authors'][2]['surname'] == "Taveras"
     assert d['authors'][2]['name'] == "L R Taveras"
@@ -65,5 +66,3 @@ def test_transform_grobid_ref_xml():
     assert d['volume'] == "23"
     assert d['issue'] == "2"
     assert d['journal'] == "Hernia"
-
-