import { Mutation } from 'cbioportal-utils';
import _ from 'lodash';
import * as React from 'react';

import ColumnHeader from '../column/ColumnHeader';
import { Column } from 'react-table';
import ProteinChange, {
    proteinChangeSortMethod,
} from '../column/ProteinChange';
import { annotationSortMethod } from '../column/Annotation';
import { gnomadSortMethod } from '../column/Gnomad';
import { clinvarSortMethod } from '../column/ClinvarInterpretation';
import MutationType from '../column/MutationType';
import { MutationStatus } from '../column/MutationStatus';
import { dbsnpSortMethod } from '../column/Dbsnp';
import { hgvscSortMethod } from '../column/Hgvsc';
import { hgvsgSortMethod } from '../column/Hgvsg';
import { signalSortMethod } from '../column/Signal';

export enum MutationColumn {
    PROTEIN_CHANGE = 'proteinChange',
    ANNOTATION = 'annotation',
    MUTATION_STATUS = 'mutationStatus',
    MUTATION_TYPE = 'mutationType',
    CHROMOSOME = 'chromosome',
    START_POSITION = 'startPosition',
    END_POSITION = 'endPosition',
    REFERENCE_ALLELE = 'referenceAllele',
    VARIANT_ALLELE = 'variantAllele',
    HGVSG = 'hgvsg',
    HGVSC = 'hgvsc',
    GNOMAD = 'gnomad',
    CLINVAR = 'clinvar',
    DBSNP = 'dbsnp',
    SIGNAL = 'signal',
}

export enum MutationColumnName {
    PROTEIN_CHANGE = 'Protein Change',
    ANNOTATION = 'Annotation',
    MUTATION_STATUS = 'Mutation Status',
    MUTATION_TYPE = 'Mutation Type',
    CHROMOSOME = 'Chromosome',
    START_POSITION = 'Start Pos',
    END_POSITION = 'End Pos',
    REFERENCE_ALLELE = 'Ref',
    VARIANT_ALLELE = 'Var',
    HGVSG = 'HGVSg',
    HGVSC = 'HGVSc',
    GNOMAD = 'gnomAD',
    CLINVAR = 'ClinVar',
    DBSNP = 'dbSNP',
    SIGNAL = 'SIGNAL',
}

export function rightAlignedCell(cellProps: any) {
    return <span className="pull-right mr-3">{cellProps.value}</span>;
}

export const MUTATION_COLUMN_HEADERS = {
    [MutationColumn.PROTEIN_CHANGE]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.PROTEIN_CHANGE}
                </span>
            }
        />
    ),
    [MutationColumn.ANNOTATION]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.ANNOTATION}
                </span>
            }
        />
    ),
    [MutationColumn.MUTATION_STATUS]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.MUTATION_STATUS}
                </span>
            }
        />
    ),
    [MutationColumn.MUTATION_TYPE]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.MUTATION_TYPE}
                </span>
            }
        />
    ),
    [MutationColumn.CHROMOSOME]: (
        <ColumnHeader
            headerContent={
                <span className="pull-right mr-3">
                    {MutationColumnName.CHROMOSOME}
                </span>
            }
        />
    ),
    [MutationColumn.START_POSITION]: (
        <ColumnHeader
            headerContent={
                <span className="pull-right mr-3">
                    {MutationColumnName.START_POSITION}
                </span>
            }
        />
    ),
    [MutationColumn.END_POSITION]: (
        <ColumnHeader
            headerContent={
                <span className="pull-right mr-3">
                    {MutationColumnName.END_POSITION}
                </span>
            }
        />
    ),
    [MutationColumn.REFERENCE_ALLELE]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.REFERENCE_ALLELE}
                </span>
            }
            overlay={<span>Reference Allele</span>}
        />
    ),
    [MutationColumn.VARIANT_ALLELE]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.VARIANT_ALLELE}
                </span>
            }
            overlay={<span>Variant Allele</span>}
        />
    ),
    [MutationColumn.HGVSG]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">{MutationColumnName.HGVSG}</span>
            }
        />
    ),
    [MutationColumn.HGVSC]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">{MutationColumnName.HGVSC}</span>
            }
        />
    ),
    [MutationColumn.GNOMAD]: (
        <ColumnHeader
            headerContent={
                <span className="pull-right mr-3">
                    {MutationColumnName.GNOMAD}{' '}
                    <i className="fa fa-info-circle" />
                </span>
            }
            overlay={
                <span>
                    <a
                        href="https://gnomad.broadinstitute.org/"
                        target="_blank"
                    >
                        gnomAD
                    </a>{' '}
                    population allele frequencies. Overall population allele
                    frequency is shown. Hover over a frequency to see the
                    frequency for each specific population.
                </span>
            }
        />
    ),
    [MutationColumn.CLINVAR]: (
        <ColumnHeader
            headerContent={
                <span className="pull-left">
                    {MutationColumnName.CLINVAR}{' '}
                    <i className="fa fa-info-circle" />
                </span>
            }
            overlay={
                <span>
                    <a
                        href="https://www.ncbi.nlm.nih.gov/clinvar/"
                        target="_blank"
                    >
                        ClinVar
                    </a>{' '}
                    aggregates information about genomic variation and its
                    relationship to human health.
                </span>
            }
        />
    ),
    [MutationColumn.DBSNP]: (
        <ColumnHeader
            headerContent={
                <span className="pull-right mr-3">
                    {MutationColumnName.DBSNP}{' '}
                    <i className="fa fa-info-circle" />
                </span>
            }
            overlay={
                <span>
                    The Single Nucleotide Polymorphism Database (
                    <a href="https://www.ncbi.nlm.nih.gov/snp/" target="_blank">
                        dbSNP
                    </a>
                    ) is a free public archive for genetic variation within and
                    across different species.
                    <br />
                    NOTE: Currently only SNPs, single base deletions and
                    insertions are supported.
                </span>
            }
        />
    ),
    [MutationColumn.SIGNAL]: (
        <ColumnHeader
            headerContent={
                <span className="pull-right mr-3">
                    {MutationColumnName.SIGNAL}{' '}
                    <i className="fa fa-info-circle" />
                </span>
            }
            overlay={
                <span>
                    Prevalence of germline mutations in cancer patients from{' '}
                    <a href="https://www.signaldb.org/" target="_blank">
                        SIGNAL
                    </a>
                </span>
            }
        />
    ),
};

/**
 * These default columns only include static props.
 * So, for some columns, like Annotation, no default accessor or Cell (render) properties included.
 */
export const MUTATION_COLUMNS_DEFINITION = {
    [MutationColumn.PROTEIN_CHANGE]: {
        id: MutationColumn.PROTEIN_CHANGE,
        name: MutationColumnName.PROTEIN_CHANGE,
        accessor: MutationColumn.PROTEIN_CHANGE,
        searchable: true,
        Cell: (column: any) => <ProteinChange mutation={column.original} />,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.PROTEIN_CHANGE],
        sortMethod: proteinChangeSortMethod,
    },
    [MutationColumn.ANNOTATION]: {
        id: MutationColumn.ANNOTATION,
        name: MutationColumnName.ANNOTATION,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.ANNOTATION],
        sortMethod: annotationSortMethod,
    },
    [MutationColumn.MUTATION_TYPE]: {
        id: MutationColumn.MUTATION_TYPE,
        name: MutationColumnName.MUTATION_TYPE,
        accessor: MutationColumn.MUTATION_TYPE,
        searchable: true,
        Cell: (column: any) => <MutationType mutation={column.original} />,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.MUTATION_TYPE],
    },
    [MutationColumn.MUTATION_STATUS]: {
        id: MutationColumn.MUTATION_STATUS,
        name: MutationColumnName.MUTATION_STATUS,
        accessor: MutationColumn.MUTATION_STATUS,
        searchable: true,
        Cell: (column: any) => <MutationStatus mutation={column.original} />,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.MUTATION_STATUS],
    },
    [MutationColumn.CHROMOSOME]: {
        id: MutationColumn.CHROMOSOME,
        name: MutationColumnName.CHROMOSOME,
        accessor: MutationColumn.CHROMOSOME,
        searchable: true,
        Cell: rightAlignedCell,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.CHROMOSOME],
        show: false,
    },
    [MutationColumn.START_POSITION]: {
        id: MutationColumn.START_POSITION,
        name: MutationColumnName.START_POSITION,
        accessor: MutationColumn.START_POSITION,
        searchable: true,
        Cell: rightAlignedCell,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.START_POSITION],
        show: false,
    },
    [MutationColumn.END_POSITION]: {
        id: MutationColumn.END_POSITION,
        name: MutationColumnName.END_POSITION,
        accessor: MutationColumn.END_POSITION,
        searchable: true,
        Cell: rightAlignedCell,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.END_POSITION],
        show: false,
    },
    [MutationColumn.REFERENCE_ALLELE]: {
        id: MutationColumn.REFERENCE_ALLELE,
        name: MutationColumnName.REFERENCE_ALLELE,
        accessor: MutationColumn.REFERENCE_ALLELE,
        searchable: true,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.REFERENCE_ALLELE],
        show: false,
    },
    [MutationColumn.VARIANT_ALLELE]: {
        id: MutationColumn.VARIANT_ALLELE,
        name: MutationColumnName.VARIANT_ALLELE,
        accessor: MutationColumn.VARIANT_ALLELE,
        searchable: true,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.VARIANT_ALLELE],
        show: false,
    },
    [MutationColumn.HGVSG]: {
        id: MutationColumn.HGVSG,
        name: MutationColumnName.HGVSG,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.HGVSG],
        sortMethod: hgvsgSortMethod,
    },
    [MutationColumn.HGVSC]: {
        id: MutationColumn.HGVSC,
        name: MutationColumnName.HGVSC,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.HGVSC],
        sortMethod: hgvscSortMethod,
    },
    [MutationColumn.GNOMAD]: {
        id: MutationColumn.GNOMAD,
        name: MutationColumnName.GNOMAD,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.GNOMAD],
        sortMethod: gnomadSortMethod,
    },
    [MutationColumn.CLINVAR]: {
        id: MutationColumn.CLINVAR,
        name: MutationColumnName.CLINVAR,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.CLINVAR],
        sortMethod: clinvarSortMethod,
        show: false,
    },
    [MutationColumn.DBSNP]: {
        id: MutationColumn.DBSNP,
        name: MutationColumnName.DBSNP,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.DBSNP],
        sortMethod: dbsnpSortMethod,
        show: false,
    },
    [MutationColumn.SIGNAL]: {
        id: MutationColumn.SIGNAL,
        name: MutationColumnName.SIGNAL,
        Header: MUTATION_COLUMN_HEADERS[MutationColumn.SIGNAL],
        sortMethod: signalSortMethod,
        show: false,
    },
};

export const DEFAULT_MUTATION_COLUMNS = [
    MUTATION_COLUMNS_DEFINITION[MutationColumn.PROTEIN_CHANGE],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.MUTATION_TYPE],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.MUTATION_STATUS],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.CHROMOSOME],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.START_POSITION],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.END_POSITION],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.REFERENCE_ALLELE],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.VARIANT_ALLELE],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.HGVSG],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.HGVSC],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.CLINVAR],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.GNOMAD],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.DBSNP],
    MUTATION_COLUMNS_DEFINITION[MutationColumn.SIGNAL],
];

export function mergeColumns(
    defaultColumns: Column<Partial<Mutation>>[],
    customColumns: Column<Partial<Mutation>>[]
) {
    const merged: Column<Partial<Mutation>>[] = [];
    const overrides: Column<Partial<Mutation>>[] = [];

    defaultColumns.forEach(column => {
        const colOverride = customColumns.find(c => c.id === column.id);
        merged.push(colOverride || column);

        if (colOverride) {
            overrides.push(colOverride);
        }
    });

    return [...merged, ..._.difference(customColumns, overrides)];
}