"""RDF utilities

This module is a collection of functions that handle SPARQL queries.

"""
from typing import Tuple
from string import Template
from urllib.parse import unquote
from urllib.parse import urlparse

from SPARQLWrapper import JSON, SPARQLWrapper
from pymonad.maybe import Just

from gn3.monads import MonadicDict


RDF_PREFIXES = """PREFIX dct: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
PREFIX gn: <http://genenetwork.org/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX publication: <http://genenetwork.org/publication/>
"""


def sparql_query(
        sparql_conn: SPARQLWrapper, query: str,
) -> Tuple[MonadicDict, ...]:
    """Run a SPARQL query and return the bound variables."""
    def __add_value_to_dict(key, value, my_dict):
        _values = set()
        if key in my_dict:
            if isinstance(my_dict[key], list):
                _values = set(my_dict[key])
            else:
                _values = set([my_dict[key]])
            _values.add(value)
        if _values:
            return list(_values)
        return value

    sparql_conn.setQuery(query)
    sparql_conn.setReturnFormat(JSON)
    parsed_response: dict = {}
    results = sparql_conn.queryAndConvert()["results"]["bindings"]  # type: ignore
    if results:
        for result in results:
            if "s" in result:  # A CONSTRUCT
                key = get_url_local_name(
                    result["p"]["value"]  # type: ignore
                )
                value = result["o"]["value"]  # type: ignore
                parsed_response[key] = __add_value_to_dict(
                    key, value, parsed_response
                )
            elif "key" in result:  # A SELECT
                parsed_response[
                    result["key"]  # type: ignore
                ] = __add_value_to_dict(
                    result["key"], result["value"],  # type: ignore
                    parsed_response
                )
    return (MonadicDict(parsed_response),)


def get_url_local_name(string: str) -> str:
    """Get the last item after a '/" from a URL"""
    if string.startswith("http"):
        url = urlparse(string)
        return unquote(url.path).rpartition("/")[-1]
    return string


def get_dataset_metadata(
        sparql_conn: SPARQLWrapper, name: str
) -> MonadicDict:
    """Return info about dataset with a given NAME"""
    __metadata_query = """
$prefix

CONSTRUCT {
    gn:dataset ?datasetTerm ?datasetValue .
    gn:dataset ?platformName ?platform_name .
    gn:dataset gn:normalization ?normalization .
    gn:dataset gn:investigatorName ?investigatorName .
    gn:dataset gn:investigatorWebUrl ?investigatorWebUrl .
    gn:dataset gn:tissueName ?tissueName .
    gn:dataset gn:organism ?speciesDisplayName .
    gn:dataset gn:organismUrl ?ncbiReference .
    gn:dataset gn:inbredSetName ?inbredSetName .
    gn:dataset gn:geoPlatformUrl ?geoPlatform .
    gn:dataset gn:platformName ?platform_name .
} WHERE {
    ?subClass rdf:subClassOf gn:dataset .
    ?dataset rdf:type ?subclass ;
             gn:name "$name";
             ?datasetTerm ?datasetValue .
    OPTIONAL {
        ?dataset gn:datasetOfInvestigator ?investigator .
        ?investigator foaf:name ?investigatorName .
        ?investigator foaf:homepage ?investigatorWebUrl .
    } .
    OPTIONAL{
        ?dataset gn:normalization ?normalizationType .
        ?normalizationType gn:name ?normalization .
    } .
    OPTIONAL{
        ?dataset gn:datasetOfSpecies ?species .
        ?species gn:displayName ?speciesDisplayName .
        ?species gn:organism ?ncbiReference .
    } .
    OPTIONAL {
        ?dataset gn:datasetOfInbredSet ?inbredSet .
        ?inbredSet gn:binomialName ?inbredSetName .
        ?inbredSet gn:inbredSetOfSpecies ?species .
        ?species gn:displayName ?speciesDisplayName .
        ?species gn:organism ?ncbiReference .
    } .
    OPTIONAL{
        ?dataset gn:datasetOfPlatform ?platform .
        ?platform gn:name ?platform_name .
        ?platform gn:geoPlatform ?geoPlatform .
    } .
    OPTIONAL{
        ?dataset gn:datasetOfTissue ?tissue .
        ?tissue gn:name ?tissueName .
    } .
    VALUES ?datasetTerm {
        dct:created gn:aboutCases gn:aboutDataProcessing gn:aboutPlatform
        gn:aboutTissue gn:accessionId gn:acknowledgment gn:citation
        gn:contributors gn:datasetGroup gn:datasetOfinvestigator
        gn:experimentDesign gn:geoSeries gn:name gn:notes
        gn:specifics gn:summary gn:title gn:publicationTitle
        gn:datasetStatusName gn:datasetOfOrganization
    }
}
"""
    response: MonadicDict = MonadicDict()
    for key, value in sparql_query(
            sparql_conn,
            Template(__metadata_query)
            .substitute(
                prefix=RDF_PREFIXES,
                name=name
            )
    )[0].items():
        response[key] = value
        if isinstance(value, str) and not (
                key.endswith("Url") or key == "geoSeries"
        ):
            response[key] = value.map(get_url_local_name)  # type: ignore
    return response
    return response


def get_trait_metadata(
        sparql_conn: SPARQLWrapper,
        trait_name: str,
        dataset_name: str
):
    """Return metadata about a given trait"""
    __metadata_query = """
PREFIX gn: <http://genenetwork.org/>

SELECT strafter((str(?key)), "http://genenetwork.org/sampledata:") as ?key
    ?value WHERE {
    gn:sampledata_$trait_name gn:sampledata:dataset "$dataset_name" .
    gn:sampledata_$trait_name ?key ?value .
}
"""
    result: MonadicDict = MonadicDict()
    for _r in sparql_query(
            sparql_conn,
            Template(__metadata_query)
            .substitute(trait_name=trait_name,
                        dataset_name=dataset_name)
    ):
        _key = _r["key"].bind(lambda x: x["value"])  # type:ignore
        if _key:
            result[_key] = _r["value"].bind(lambda x: Just(x["value"]))  # type:ignore
    return result