# -*- coding: utf-8 -*-

"""Importer for Hetionet JSON."""

import bz2
import json
import logging
from typing import Any, Mapping, Set, Tuple, Union

import pystow
from tqdm.autonotebook import tqdm

from .constants import (
    ACTIVATES_ACTIONS,
    BINDS_ACTIONS,
    COMPOUND,
    DSL_MAP,
    GENE,
    HETIONET_PUBMED,
    INHIBITS_ACTIONS,
    PHARMACOLOGICAL_CLASS,
    QUALIFIED_MAPPING,
    REGULATES_ACTIONS,
    UNQUALIFIED_MAPPING,
)
from ...dsl import Abundance, Protein
from ...struct import BELGraph

__all__ = [
    "get_hetionet",
    "from_hetionet_json",
    "from_hetionet_gz",
    "from_hetionet_file",
]

logger = logging.getLogger(__name__)

JSON_BZ2_URL = "https://github.com/hetio/hetionet/raw/master/hetnet/json/hetionet-v1.0.json.bz2"


def get_hetionet() -> BELGraph:
    """Get Hetionet from GitHub, cache, and convert to BEL."""
    path = pystow.ensure("bio2bel", "hetionet", url=JSON_BZ2_URL)
    return from_hetionet_gz(path.as_posix())


def from_hetionet_gz(path: str) -> BELGraph:
    """Get Hetionet from its JSON GZ file."""
    logger.info("opening %s", path)
    with bz2.open(path) as file:
        return from_hetionet_file(file)


def from_hetionet_file(file) -> BELGraph:
    """Get Hetionet from a JSON file."""
    logger.info("parsing json from %s", file)
    j = json.load(file)
    logger.info("converting hetionet dict to BEL")
    return from_hetionet_json(j)


def from_hetionet_json(
    hetionet_dict: Mapping[str, Any],
    use_tqdm: bool = True,
) -> BELGraph:
    """Convert a Hetionet dictionary to a BEL graph."""
    graph = BELGraph(  # FIXME what metadata is appropriate?
        name="Hetionet",
        version="1.0",
        authors="Daniel Himmelstein",
    )
    # FIXME add namespaces
    # graph.namespace_pattern.update({})

    kind_identifier_to_name = {(x["kind"], x["identifier"]): x["name"] for x in hetionet_dict["nodes"]}

    edges = hetionet_dict["edges"]

    if use_tqdm:
        edges = tqdm(edges, desc="Converting Hetionet", unit_scale=True)
        it_logger = edges.write
    else:
        it_logger = logger.info

    for edge in edges:
        _add_edge(graph, edge, kind_identifier_to_name, it_logger)

    return graph


def _get_node(edge, key, kind_identifier_to_name) -> Union[Tuple[None, None, None, None], Tuple[str, str, str, str]]:
    node_type, node_identifier = edge[key]
    namespace = DSL_MAP.get(node_type)
    if namespace is None:
        return None, None, None, None
    node_name = kind_identifier_to_name[node_type, node_identifier]
    node_identifier = str(node_identifier)

    if node_identifier.lower().startswith(namespace):
        node_identifier = node_identifier[1 + len(namespace) :]  # remove redundant prefix

    return node_type, namespace, node_identifier, node_name


def _add_edge(  # noqa: C901
    graph,
    edge,
    kind_identifier_to_name,
    it_logger,
) -> Union[None, str, Set[str]]:
    source_type, source_ns, source_identifier, source_name = _get_node(edge, "source_id", kind_identifier_to_name)
    target_type, target_ns, target_identifier, target_name = _get_node(edge, "target_id", kind_identifier_to_name)
    if source_type is None or target_type is None:
        return

    kind = edge["kind"]

    # direction = e['direction']
    data = edge["data"]
    if "unbiased" in data:
        del data["unbiased"]

    annotations = {}
    if "source" in data:
        source = data.pop("source")
        annotations["source"] = {source: True}
    elif "sources" in data:
        annotations["source"] = {source: True for source in data.pop("sources")}
    else:
        pass
        # it_logger(f'Missing source for {source_identifier}-{kind}-{target_identifier}\n{e}')

    if "pubmed_ids" in data:
        citations = list(data.pop("pubmed_ids"))
    else:
        citations = [HETIONET_PUBMED]

    for k, v in data.items():
        if k in {"actions", "urls", "subtypes"}:
            continue  # handled explicitly later
        if not isinstance(v, (str, int, bool, float)):
            it_logger(
                "Unhandled: {source_identifier}-{kind}-{target_identifier} {k}: {v}".format(
                    source_identifier=source_identifier,
                    kind=kind,
                    target_identifier=target_identifier,
                    k=k,
                    v=v,
                )
            )
            continue
        annotations[k] = {v: True}

    for _h_type, h_dsl, _r, _t_type, t_dsl, f in QUALIFIED_MAPPING:
        if source_type != _h_type or kind != _r or target_type != _t_type:
            continue
        rv = set()
        for citation in citations:
            key = f(
                graph,
                h_dsl(namespace=source_ns, identifier=source_identifier, name=source_name),
                t_dsl(namespace=target_ns, identifier=target_identifier, name=target_name),
                citation=citation,
                evidence="",
                annotations=annotations,
            )
            rv.add(key)
        return rv

    for _h_type, h_dsl, _r, _t_type, t_dsl, f in UNQUALIFIED_MAPPING:
        if source_type == _h_type and kind == _r and target_type == _t_type:
            return f(
                graph,
                h_dsl(namespace=source_ns, identifier=source_identifier, name=source_name),
                t_dsl(namespace=target_ns, identifier=target_identifier, name=target_name),
            )

    def _check(_source_type: str, _kind: str, _target_type: str) -> bool:
        """Check the metaedge."""
        return kind == _kind and source_type == _source_type and target_type == _target_type

    if _check(COMPOUND, "binds", GENE):
        drug = Abundance(namespace="drugbank", name=source_name, identifier=source_identifier)
        protein = Protein(namespace="ncbigene", name=target_name, identifier=target_identifier)

        rv = set()
        for action in data.get("actions", []):
            action = action.lower()
            if action in ACTIVATES_ACTIONS:
                key = graph.add_directly_activates(
                    drug,
                    protein,
                    citation=HETIONET_PUBMED,
                    evidence="",
                    annotations=annotations,
                )
            elif action in INHIBITS_ACTIONS:
                key = graph.add_directly_inhibits(
                    drug,
                    protein,
                    citation=HETIONET_PUBMED,
                    evidence="",
                    annotations=annotations,
                )
            elif action in REGULATES_ACTIONS:
                key = graph.add_regulates(
                    drug,
                    protein,
                    citation=HETIONET_PUBMED,
                    evidence="",
                    annotations=annotations,
                )
            elif action in BINDS_ACTIONS:
                key = graph.add_binds(
                    drug,
                    protein,
                    citation=HETIONET_PUBMED,
                    evidence="",
                    annotations=annotations,
                )
            else:
                key = graph.add_binds(
                    drug,
                    protein,
                    citation=HETIONET_PUBMED,
                    evidence="",
                    annotations=annotations,
                )
                it_logger(
                    "Unhandled action for {source_identifier}-{kind}-{target_identifier}: {action}".format(
                        source_identifier=source_identifier,
                        kind=kind,