"""
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