import pytest
from bs4 import BeautifulSoup
from fixtures import *

from fatcat_tools.importers import Bs4XmlLargeFilePusher, PubmedImporter


@pytest.fixture(scope="function")
def pubmed_importer(api):
    with open("tests/files/ISSN-to-ISSN-L.snip.txt", "r") as issn_file:
        yield PubmedImporter(
            api,
            issn_file,
            bezerk_mode=True,
            lookup_refs=True,
        )


@pytest.fixture(scope="function")
def pubmed_importer_existing(api):
    with open("tests/files/ISSN-to-ISSN-L.snip.txt", "r") as issn_file:
        yield PubmedImporter(
            api,
            issn_file,
            bezerk_mode=False,
            lookup_refs=True,
        )


def test_pubmed_importer(pubmed_importer):
    last_index = pubmed_importer.api.get_changelog(limit=1)[0].index
    with open("tests/files/pubmedsample_2019.xml", "r") as f:
        pubmed_importer.bezerk_mode = True
        counts = Bs4XmlLargeFilePusher(pubmed_importer, f, ["PubmedArticle"]).run()
    assert counts["insert"] == 176
    assert counts["exists"] == 0
    assert counts["skip"] == 0

    # fetch most recent editgroup
    change = pubmed_importer.api.get_changelog_entry(index=last_index + 1)
    eg = change.editgroup
    assert eg.description
    assert "pubmed" in eg.description.lower()
    assert eg.extra["git_rev"]
    assert "fatcat_tools.PubmedImporter" in eg.extra["agent"]

    last_index = pubmed_importer.api.get_changelog(limit=1)[0].index
    with open("tests/files/pubmedsample_2019.xml", "r") as f:
        pubmed_importer.bezerk_mode = False
        pubmed_importer.reset()
        counts = Bs4XmlLargeFilePusher(pubmed_importer, f, ["PubmedArticle"]).run()
    assert counts["insert"] == 0
    assert counts["exists"] == 176
    assert counts["skip"] == 0
    assert last_index == pubmed_importer.api.get_changelog(limit=1)[0].index


def test_pubmed_xml_parse(pubmed_importer):
    with open("tests/files/pubmedsample_2019.xml", "r") as f:
        soup = BeautifulSoup(f, "xml")
        r1 = pubmed_importer.parse_record(soup.find_all("PubmedArticle")[0])
        r2 = pubmed_importer.parse_record(soup.find_all("PubmedArticle")[-1])

    assert r1.title == "Hospital debt management and cost reimbursement"
    assert r1.subtitle is None
    assert r1.original_title is None
    assert r1.publisher is None
    assert r1.release_type == "article-journal"
    assert r1.release_stage == "published"
    assert r1.license_slug is None
    assert r1.ext_ids.doi is None
    assert r1.ext_ids.pmid == "973217"
    assert r1.language == "en"
    assert r1.volume == "3"
    assert r1.issue == "1"
    assert r1.pages == "69-81"
    assert r1.release_date is None  # not "1976-12-03", which is medline ingest date
    assert r1.release_year == 1976
    # matched by ISSN, so shouldn't be in there?
    # assert extra['container_name'] == "Abstracts of the Papers Communicated to the Royal Society of London"
    assert len(r1.contribs) == 1

    assert r1.contribs[0].raw_name == "F R Blume"
    assert r1.contribs[0].given_name == "F R"
    assert r1.contribs[0].surname == "Blume"

    print(r1.extra)
    assert r1.extra["pubmed"]["pub_types"] == ["Journal Article"]
    assert not r1.refs

    assert (
        r2.title
        == "Synthesis and Antibacterial Activity of Metal(loid) Nanostructures by Environmental Multi-Metal(loid) Resistant Bacteria and Metal(loid)-Reducing Flavoproteins"
    )
    assert r2.subtitle is None
    assert r2.original_title is None
    assert r2.publisher is None
    assert r2.release_type == "article-journal"
    assert r2.release_stage == "published"
    assert r2.license_slug is None
    assert r2.ext_ids.doi == "10.3389/fmicb.2018.00959"
    assert r2.ext_ids.pmid == "29869640"
    assert r2.ext_ids.pmcid == "PMC5962736"
    assert r2.language == "en"
    assert r2.volume == "9"
    assert r2.issue is None
    assert r2.pages == "959"
    assert str(r2.release_date) == "2018-05-15"
    assert r2.release_year == 2018
    # matched by ISSN, so shouldn't be in there?
    # assert extra['container_name'] == "Frontiers in microbiology"

    assert len(r2.contribs) > 3
    assert r2.contribs[0].raw_name == "Maximiliano Figueroa"
    assert r2.contribs[0].given_name == "Maximiliano"
    assert r2.contribs[0].surname == "Figueroa"
    assert (
        r2.contribs[0].raw_affiliation
        == "Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile."
    )
    assert r2.contribs[4].surname == "Muñoz-Villagrán"
    assert r2.contribs[7].surname == "Latorre"
    assert (
        r2.contribs[7].raw_affiliation
        == "Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Beauchef, Santiago, Chile."
    )
    assert r2.contribs[7].extra["more_affiliations"] == [
        "Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.",
        "Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.",
        "Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.",
    ]
    assert r2.contribs[-1].raw_name == "Felipe Arenas"

    assert r2.abstracts[0].content.startswith(
        "Microbes are suitable candidates to recover and decontaminate different environments from soluble metal ions, either via reduction"
    )
    assert r2.abstracts[0].lang == "en"

    print(r2.extra)
    assert r2.extra["pubmed"]["pub_types"] == ["Journal Article"]

    assert r2.refs[0].extra["unstructured"] == "Microbiology. 2009 Jun;155(Pt 6):1840-6"
    assert r2.refs[0].extra["pmid"] == "19383690"
    assert len(r2.refs) > 1


def test_pubmed_xml_dates(pubmed_importer):
    with open("tests/files/pubmed_31393839.xml", "r") as f:
        soup = BeautifulSoup(f, "xml")
        r1 = pubmed_importer.parse_record(soup.find_all("PubmedArticle")[0])

    assert r1.release_year == 2019


def test_pubmed_xml_parse_refs(pubmed_importer):
    """
    Tests the case of multiple nested ReferenceList/Reference objects, instead
    of a single ReferenceList with multiple Reference
    """
    with open("tests/files/pubmed_19129924.xml", "r") as f:
        soup = BeautifulSoup(f, "xml")
        r1 = pubmed_importer.parse_record(soup.find_all("PubmedArticle")[0])

    assert len(r1.refs) > 1