remove legacy grobid2json code itself

3 files changed, 0 insertions, 313 deletions

diff --git a/grobid_tei_xml/__init__.py b/grobid_tei_xml/__init__.py
index 9ddce29..8cdbefc 100644
--- a/grobid_tei_xml/__init__.py
+++ b/grobid_tei_xml/__init__.py
@@ -1,5 +1,4 @@
 __version__ = "0.1.0"
 
-from .grobid2json import teixml2json
 from .parse import parse_citations_xml, parse_document_xml
 from .types import GrobidBiblio, GrobidDocument
diff --git a/grobid_tei_xml/grobid2json.py b/grobid_tei_xml/grobid2json.py
deleted file mode 100644
index c10de7c..0000000
--- a/grobid_tei_xml/grobid2json.py
+++ /dev/null
@@ -1,201 +0,0 @@
-"""
-NOTE: this file is DEPRECATED. It is only here for testing backwards
-compatibility, and will be removed soon.
-"""
-
-import io
-import xml.etree.ElementTree as ET
-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]]:
-    if not elem:
-        return []
-    names = []
-    for author in elem.findall(".//{%s}author" % ns):
-        pn = author.find("./{%s}persName" % ns)
-        if not pn:
-            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()
-        obj: Dict[str, Any] = dict(name=full_name)
-        if given_name:
-            obj["given_name"] = given_name
-        if surname:
-            obj["surname"] = surname
-        ae = author.find("./{%s}affiliation" % ns)
-        if ae:
-            affiliation: Dict[str, Any] = dict()
-            for on in ae.findall("./{%s}orgName" % ns):
-                on_type = on.get("type")
-                if on_type:
-                    affiliation[on_type] = on.text
-            addr_e = ae.find("./{%s}address" % ns)
-            if addr_e:
-                address = dict()
-                for t in list(addr_e):
-                    address[t.tag.split("}")[-1]] = t.text
-                if address:
-                    affiliation["address"] = address
-                # affiliation['address'] = {
-                #    'post_code': addr.findtext('./{%s}postCode' % ns) or None,
-                #    'settlement': addr.findtext('./{%s}settlement' % ns) or None,
-                #    'country': addr.findtext('./{%s}country' % ns) or None,
-                # }
-            obj["affiliation"] = affiliation
-        names.append(obj)
-    return names
-
-
-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")
-    if journal["publisher"] == "":
-        journal["publisher"] = None
-    journal["issn"] = elem.findtext('.//{%s}idno[@type="ISSN"]' % ns)
-    journal["eissn"] = elem.findtext('.//{%s}idno[@type="eISSN"]' % ns)
-    journal["volume"] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
-    journal["issue"] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
-
-    # remove empty/null keys
-    keys = list(journal.keys())
-    for k in keys:
-        if not journal[k]:
-            journal.pop(k)
-    return journal
-
-
-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)
-    # Title stuff is messy in references...
-    ref["title"] = elem.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
-    other_title = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
-    if other_title:
-        if ref["title"]:
-            ref["journal"] = other_title
-        else:
-            ref["journal"] = None
-            ref["title"] = other_title
-    ref["authors"] = all_authors(elem, ns=ns)
-    ref["publisher"] = elem.findtext(f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
-    if not ref["publisher"]:
-        ref["publisher"] = elem.findtext(f".//{{{ns}}}imprint/{{{ns}}}publisher")
-    if ref["publisher"] == "":
-        ref["publisher"] = None
-    date = elem.find('.//{%s}date[@type="published"]' % ns)
-    ref["date"] = (date is not None) and date.attrib.get("when")
-    ref["volume"] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
-    ref["issue"] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
-    ref["doi"] = elem.findtext('.//{%s}idno[@type="DOI"]' % ns)
-    ref["arxiv_id"] = elem.findtext('.//{%s}idno[@type="arXiv"]' % ns)
-    if ref["arxiv_id"] and ref["arxiv_id"].startswith("arXiv:"):
-        ref["arxiv_id"] = ref["arxiv_id"][6:]
-    ref["pmcid"] = elem.findtext('.//{%s}idno[@type="PMCID"]' % ns)
-    ref["pmid"] = elem.findtext('.//{%s}idno[@type="PMID"]' % ns)
-    el = elem.find('.//{%s}biblScope[@unit="page"]' % ns)
-    if el is not None:
-        if el.attrib.get("from") and el.attrib.get("to"):
-            ref["pages"] = "{}-{}".format(el.attrib["from"], el.attrib["to"])
-        else:
-            ref["pages"] = el.text
-    el = elem.find(".//{%s}ptr[@target]" % ns)
-    if el is not None:
-        ref["url"] = el.attrib["target"]
-        # Hand correction
-        # TODO: move this elsewhere
-        if ref["url"].endswith(".Lastaccessed"):
-            ref["url"] = ref["url"].replace(".Lastaccessed", "")
-        if ref["url"].startswith("<"):
-            ref["url"] = ref["url"][1:]
-        if ">" in ref["url"]:
-            ref["url"] = ref["url"].split(">")[0]
-    else:
-        ref["url"] = None
-
-    # remove empty/null keys
-    keys = list(ref.keys())
-    for k in keys:
-        if ref[k] is None:
-            ref.pop(k)
-    return ref
-
-
-def teixml2json(content: AnyStr, encumbered: bool = True) -> Dict[str, Any]:
-
-    if isinstance(content, str):
-        tree = ET.parse(io.StringIO(content))
-    elif isinstance(content, bytes):
-        tree = ET.parse(io.BytesIO(content))
-
-    info: Dict[str, Any] = dict()
-
-    # print(content)
-    # print(content.getvalue())
-    tei = tree.getroot()
-
-    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]
-    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"))
-    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["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")):
-        ref = biblio_info(bs)
-        ref["index"] = i
-        refs.append(ref)
-    info["citations"] = refs
-
-    text = tei.find(".//{%s}text" % (ns))
-    # print(text.attrib)
-    if text and text.attrib.get("{%s}lang" % xml_ns):
-        info["language_code"] = text.attrib["{%s}lang" % xml_ns]  # xml:lang
-
-    if encumbered:
-        el = tei.find(f".//{{{ns}}}profileDesc/{{{ns}}}abstract")
-        info["abstract"] = (el or None) and " ".join(el.itertext()).strip()
-        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()
-        el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="annex"]')
-        info["annex"] = (el or None) and " ".join(el.itertext()).strip()
-
-    # remove empty/null keys
-    keys = list(info.keys())
-    for k in keys:
-        if not info[k]:
-            info.pop(k)
-    return info
-
-
-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 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()
-    ref = biblio_info(root, ns="")
-    if not any(ref.values()):
-        return None
-    return ref
diff --git a/tests/test_grobid2json.py b/tests/test_grobid2json.py
deleted file mode 100644
index 47ab293..0000000
--- a/tests/test_grobid2json.py
+++ /dev/null
@@ -1,111 +0,0 @@
-import json
-import xml
-
-import pytest
-
-from grobid_tei_xml.grobid2json import teixml2json, transform_grobid_ref_xml
-
-
-def test_small_xml() -> None:
-
-    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())
-
-    assert teixml2json(tei_xml) == json_form
-
-
-def test_invalid_xml() -> None:
-
-    with pytest.raises(xml.etree.ElementTree.ParseError):
-        teixml2json("this is not XML")
-    with pytest.raises(ValueError):
-        teixml2json("<xml></xml>")
-
-
-def test_grobid_teixml2json() -> None:
-
-    with open("tests/files/example_grobid.tei.xml", "r") as f:
-        blob = f.read()
-
-    obj = teixml2json(blob, True)
-
-    assert 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["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."""
-
-
-def test_transform_grobid_ref_xml() -> None:
-    citation_xml = """
-<biblStruct >
-    <analytic>
-        <title level="a" type="main">Mesh migration following abdominal hernia repair: a comprehensive review</title>
-        <author>
-            <persName
-                xmlns="http://www.tei-c.org/ns/1.0">
-                <forename type="first">H</forename>
-                <forename type="middle">B</forename>
-                <surname>Cunningham</surname>
-            </persName>
-        </author>
-        <author>
-            <persName
-                xmlns="http://www.tei-c.org/ns/1.0">
-                <forename type="first">J</forename>
-                <forename type="middle">J</forename>
-                <surname>Weis</surname>
-            </persName>
-        </author>
-        <author>
-            <persName
-                xmlns="http://www.tei-c.org/ns/1.0">
-                <forename type="first">L</forename>
-                <forename type="middle">R</forename>
-                <surname>Taveras</surname>
-            </persName>
-        </author>
-        <author>
-            <persName
-                xmlns="http://www.tei-c.org/ns/1.0">
-                <forename type="first">S</forename>
-                <surname>Huerta</surname>
-            </persName>
-        </author>
-        <idno type="DOI">10.1007/s10029-019-01898-9</idno>
-        <idno type="PMID">30701369</idno>
-    </analytic>
-    <monogr>
-        <title level="j">Hernia</title>
-        <imprint>
-            <biblScope unit="volume">23</biblScope>
-            <biblScope unit="issue">2</biblScope>
-            <biblScope unit="page" from="235" to="243" />
-            <date type="published" when="2019-01-30" />
-        </imprint>
-    </monogr>
-</biblStruct>"""
-
-    d = transform_grobid_ref_xml(citation_xml)
-    assert d
-    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"
-    assert d['doi'] == "10.1007/s10029-019-01898-9"
-    assert d['pmid'] == "30701369"
-    assert d['date'] == "2019-01-30"
-    assert d['pages'] == "235-243"
-    assert d['volume'] == "23"
-    assert d['issue'] == "2"
-    assert d['journal'] == "Hernia"