import {z} from 'zod'

export type GetApiAllParticipantsOptions = {baseUrl?: string | undefined, fetch?: typeof fetch | undefined};

export const hexId = z.string();

export const wGS = z.array(z.object({study_accession: z.string().optional(), secondary_study_accession: z.string().optional(), sample_accession: z.string().optional(), secondary_sample_accession: z.string().optional(), experiment_accession: z.string().optional(), run_accession: z.string().optional(), submission_accession: z.string().optional(), tax_id: z.string().optional(), scientific_name: z.string().optional(), instrument_platform: z.string().optional(), instrument_model: z.string().optional(), library_name: z.string().optional(), nominal_length: z.string().optional(), library_layout: z.string().optional(), library_strategy: z.string().optional(), library_source: z.string().optional(), library_selection: z.string().optional(), read_count: z.string().optional(), base_count: z.string().optional(), center_name: z.string().optional(), first_public: z.string().optional(), last_updated: z.string().optional(), experiment_title: z.string().optional(), study_title: z.string().optional(), study_alias: z.string().optional(), experiment_alias: z.string().optional(), run_alias: z.string().optional(), fastq_bytes: z.string().optional(), fastq_md5: z.string().optional(), fastq_ftp: z.string().optional(), fastq_aspera: z.string().optional(), fastq_galaxy: z.string().optional(), submitted_bytes: z.string().optional(), submitted_md5: z.string().optional(), submitted_ftp: z.string().optional(), submitted_aspera: z.string().optional(), submitted_galaxy: z.string().optional(), submitted_format: z.string().optional(), sra_bytes: z.string().optional(), sra_md5: z.string().optional(), sra_ftp: z.string().optional(), sra_aspera: z.string().optional(), sra_galaxy: z.string().optional(), cram_index_ftp: z.string().optional(), cram_index_aspera: z.string().optional(), cram_index_galaxy: z.string().optional(), sample_alias: z.string().optional(), broker_name: z.string().optional(), sample_title: z.string().optional(), nominal_sdev: z.string().optional(), first_created: z.string().optional(), type: z.string().optional(), meta_data_source: z.string().optional()}));

export const variant = z.array(z.object({test: z.string().optional(), analysis_accession: z.string().optional(), study_accession: z.string().optional(), secondary_study_accession: z.string().optional(), sample_accession: z.string().optional(), secondary_sample_accession: z.string().optional(), analysis_title: z.string().optional(), analysis_type: z.string().optional(), center_name: z.string().optional(), first_public: z.string().optional(), last_updated: z.string().optional(), study_title: z.string().optional(), tax_id: z.string().optional(), scientific_name: z.string().optional(), analysis_alias: z.string().optional(), study_alias: z.string().optional(), submitted_bytes: z.string().optional(), submitted_md5: z.string().optional(), submitted_ftp: z.string().optional(), submitted_aspera: z.string().optional(), submitted_galaxy: z.string().optional(), sample_alias: z.string().optional(), broker_name: z.string().optional(), sample_title: z.string().optional(), type: z.string().optional(), meta_data_source: z.string().optional()}));

export const genotype = z.array(z.object({published: z.string().optional(), file_source: z.string().optional(), date: z.string().optional(), description: z.string().optional(), download_url: z.string().optional(), data_type: z.string().optional(), name: z.string().optional(), pgp_hex_id: z.string().optional(), type: z.string().optional()}));

export const wGBS = z.array(z.object({study_accession: z.string().optional(), secondary_study_accession: z.string().optional(), sample_accession: z.string().optional(), secondary_sample_accession: z.string().optional(), experiment_accession: z.string().optional(), run_accession: z.string().optional(), submission_accession: z.string().optional(), tax_id: z.string().optional(), scientific_name: z.string().optional(), instrument_platform: z.string().optional(), instrument_model: z.string().optional(), library_name: z.string().optional(), nominal_length: z.string().optional(), library_layout: z.string().optional(), library_strategy: z.string().optional(), library_source: z.string().optional(), library_selection: z.string().optional(), read_count: z.string().optional(), base_count: z.string().optional(), center_name: z.string().optional(), first_public: z.string().optional(), last_updated: z.string().optional(), experiment_title: z.string().optional(), study_title: z.string().optional(), study_alias: z.string().optional(), experiment_alias: z.string().optional(), run_alias: z.string().optional(), fastq_bytes: z.string().optional(), fastq_md5: z.string().optional(), fastq_ftp: z.string().optional(), fastq_aspera: z.string().optional(), fastq_galaxy: z.string().optional(), submitted_bytes: z.string().optional(), submitted_md5: z.string().optional(), submitted_ftp: z.string().optional(), submitted_aspera: z.string().optional(), submitted_galaxy: z.string().optional(), submitted_format: z.string().optional(), sra_bytes: z.string().optional(), sra_md5: z.string().optional(), sra_ftp: z.string().optional(), sra_aspera: z.string().optional(), sra_galaxy: z.string().optional(), cram_index_ftp: z.string().optional(), cram_index_aspera: z.string().optional(), cram_index_galaxy: z.string().optional(), sample_alias: z.string().optional(), broker_name: z.string().optional(), sample_title: z.string().optional(), nominal_sdev: z.string().optional(), first_created: z.string().optional(), type: z.string().optional(), meta_data_source: z.string().optional()}));

export const methylationArrayData = z.array(z.object({source_name: z.string().optional(), characteristicsorganism: z.string().optional(), characteristicsindividual: z.string().optional(), commentbiosd_sample: z.string().optional(), characteristicsorganism_part: z.string().optional(), characteristicsage: z.string().optional(), unittime_unit: z.string().optional(), term_source_ref: z.string().optional(), term_accession_number: z.string().optional(), characteristicssex: z.string().optional(), characteristicssmoking_status: z.string().optional(), commentupdate_information: z.string().optional(), material_type: z.string().optional(), protocol_ref: z.string().optional(), extract_name: z.string().optional(), labeled_extract_name: z.string().optional(), label: z.string().optional(), assay_name: z.string().optional(), technology_type: z.string().optional(), array_design_ref: z.string().optional(), array_data_file: z.string().optional(), comment_arrayexpress_ftp_file: z.string().optional(), factor_valueage: z.string().optional(), factor_value_organism_part: z.string().optional(), factor_value_smoking_status: z.string().optional(), factor_value_individual: z.string().optional(), type: z.string().optional(), accession: z.string().optional(), meta_data_source: z.string().optional()}));

export const rnaSeq = z.array(z.object({source_name: z.string().optional(), commentena_sample: z.string().optional(), commentbiosd_sample: z.string().optional(), characteristicsorganism: z.string().optional(), characteristicsdisease: z.string().optional(), characteristicssex: z.string().optional(), characteristicsindividual: z.string().optional(), characteristicsage: z.string().optional(), unittime_unit: z.string().optional(), term_source_ref: z.string().optional(), term_accession_number: z.string().optional(), characteristicsclinical_history: z.string().optional(), characteristicsorganism_part: z.string().optional(), material_type: z.string().optional(), protocol_ref: z.string().optional(), extract_name: z.string().optional(), commentlibrary_layout: z.string().optional(), commentlibrary_selection: z.string().optional(), commentlibrary_source: z.string().optional(), commentlibrary_strategy: z.string().optional(), commentnominal_length: z.string().optional(), commentnominal_sdev: z.string().optional(), commentorientation: z.string().optional(), performer: z.string().optional(), assay_name: z.string().optional(), technology_type: z.string().optional(), commentena_experiment: z.string().optional(), scan_name: z.string().optional(), commentsubmitted_file_name: z.string().optional(), commentena_run: z.string().optional(), commentfastq_uri: z.string().optional(), commentspot_length: z.string().optional(), commentread_index_1_base_coord: z.string().optional(), derived_array_data_file: z.string().optional(), comment_derived_arrayexpress_ftp_file: z.string().optional(), factor_valueclinical_history: z.string().optional(), factor_valueindividual: z.string().optional(), factor_valueprotocol: z.string().optional(), type: z.string().optional(), accession: z.string().optional(), meta_data_source: z.string().optional()}));

export const ampliconRNAseq = z.array(z.object({study_accession: z.string().optional(), secondary_study_accession: z.string().optional(), sample_accession: z.string().optional(), secondary_sample_accession: z.string().optional(), experiment_accession: z.string().optional(), run_accession: z.string().optional(), submission_accession: z.string().optional(), tax_id: z.string().optional(), scientific_name: z.string().optional(), instrument_platform: z.string().optional(), instrument_model: z.string().optional(), library_name: z.string().optional(), nominal_length: z.string().optional(), library_layout: z.string().optional(), library_strategy: z.string().optional(), library_source: z.string().optional(), library_selection: z.string().optional(), read_count: z.string().optional(), base_count: z.string().optional(), center_name: z.string().optional(), first_public: z.string().optional(), last_updated: z.string().optional(), experiment_title: z.string().optional(), study_title: z.string().optional(), study_alias: z.string().optional(), experiment_alias: z.string().optional(), run_alias: z.string().optional(), fastq_bytes: z.string().optional(), fastq_md5: z.string().optional(), fastq_ftp: z.string().optional(), fastq_aspera: z.string().optional(), fastq_galaxy: z.string().optional(), submitted_bytes: z.string().optional(), submitted_md5: z.string().optional(), submitted_ftp: z.string().optional(), submitted_aspera: z.string().optional(), submitted_galaxy: z.string().optional(), submitted_format: z.string().optional(), sra_bytes: z.string().optional(), sra_md5: z.string().optional(), sra_ftp: z.string().optional(), sra_aspera: z.string().optional(), sra_galaxy: z.string().optional(), cram_index_ftp: z.string().optional(), cram_index_aspera: z.string().optional(), cram_index_galaxy: z.string().optional(), sample_alias: z.string().optional(), broker_name: z.string().optional(), sample_title: z.string().optional(), nominal_sdev: z.string().optional(), first_created: z.string().optional(), type: z.string().optional(), meta_data_source: z.string().optional()}));

export const protonRnaSeq = z.array(z.object({study_accession: z.string().optional(), secondary_study_accession: z.string().optional(), sample_accession: z.string().optional(), secondary_sample_accession: z.string().optional(), experiment_accession: z.string().optional(), run_accession: z.string().optional(), submission_accession: z.string().optional(), tax_id: z.string().optional(), scientific_name: z.string().optional(), instrument_platform: z.string().optional(), instrument_model: z.string().optional(), library_name: z.string().optional(), nominal_length: z.string().optional(), library_layout: z.string().optional(), library_strategy: z.string().optional(), library_source: z.string().optional(), library_selection: z.string().optional(), read_count: z.string().optional(), base_count: z.string().optional(), center_name: z.string().optional(), first_public: z.string().optional(), last_updated: z.string().optional(), experiment_title: z.string().optional(), study_title: z.string().optional(), study_alias: z.string().optional(), experiment_alias: z.string().optional(), run_alias: z.string().optional(), fastq_bytes: z.string().optional(), fastq_md5: z.string().optional(), fastq_ftp: z.string().optional(), fastq_aspera: z.string().optional(), fastq_galaxy: z.string().optional(), submitted_bytes: z.string().optional(), submitted_md5: z.string().optional(), submitted_ftp: z.string().optional(), submitted_aspera: z.string().optional(), submitted_galaxy: z.string().optional(), submitted_format: z.string().optional(), sra_bytes: z.string().optional(), sra_md5: z.string().optional(), sra_ftp: z.string().optional(), sra_aspera: z.string().optional(), sra_galaxy: z.string().optional(), cram_index_ftp: z.string().optional(), cram_index_aspera: z.string().optional(), cram_index_galaxy: z.string().optional(), sample_alias: z.string().optional(), broker_name: z.string().optional(), sample_title: z.string().optional(), nominal_sdev: z.string().optional(), first_created: z.string().optional(), type: z.string().optional(), meta_data_source: z.string().optional()}));

export const dataURLs = z.array(z.object({type: z.string().optional(), download_url: z.string().optional()}));

export const pGPUKProfile = z.array(z.object({public_profile_url: z.string().optional(), deceased: z.boolean().optional(), zip: z.string().optional(), files: z.array(z.object({file_source: z.string().optional(), download_url: z.string().optional(), data_type: z.string().optional(), name: z.string().optional(), description: z.string().optional(), data: z.string().optional()})).optional(), hex: z.string().optional(), real_name: z.string().optional(), type: z.string().optional()}));

export const genomeReport = z.array(z.object({published: z.string().optional(), file_source: z.string().optional(), download_url: z.string().optional(), data_type: z.string().optional(), name: z.string().optional(), pgp_hex_id: z.string().optional(), type: z.string().optional()}));

export const methylomeReport = z.array(z.object({published: z.string().optional(), file_source: z.string().optional(), download_url: z.string().optional(), data_type: z.string().optional(), name: z.string().optional(), pgp_hex_id: z.string().optional(), type: z.string().optional()}));

export const phenotype = z.array(z.object({name: z.string().optional(), data: z.array(z.object({question: z.string().optional(), answer: z.string().optional()})).optional()}));

export const participant = z.array(z.object({wgs: wGS.optional(), variant: variant.optional(), genotype: genotype.optional(), wgbs: wGBS.optional(), meth_array: methylationArrayData.optional(), rna_seq: rnaSeq.optional(), amplicon_rna_seq: ampliconRNAseq.optional(), proton_rna_seq: protonRnaSeq.optional(), download_url: dataURLs.optional(), pgp_profile: pGPUKProfile.optional(), genome_report: genomeReport.optional(), methylome_report: methylomeReport.optional(), phenotype: phenotype.optional()}));

export const getApiAllParticipantsResponse = z.object({hex_id: hexId.optional(), data: participant.optional()});

export const validateResponse = async <Output>(
  schema: {
    readonly '~standard': {
      readonly validate: (value: unknown) => ({ readonly value: Output; readonly issues?: undefined } | { readonly issues: ReadonlyArray<{ readonly message: string; readonly path?: ReadonlyArray<PropertyKey | { readonly key: PropertyKey }> | undefined }> }) | Promise<{ readonly value: Output; readonly issues?: undefined } | { readonly issues: ReadonlyArray<{ readonly message: string; readonly path?: ReadonlyArray<PropertyKey | { readonly key: PropertyKey }> | undefined }> }>
    }
  },
  value: unknown
): Promise<Output> => {
  const result = await schema['~standard'].validate(value)

  if (result.issues !== undefined) {
    const detail = result.issues
      .map(({ message, path }) =>
        path?.length
          ? `${path.map((segment) => String(typeof segment === 'object' ? segment.key : segment)).join('.')}: ${message}`
          : message
      )
      .join('; ')

    throw new Error(`Response does not match the schema: ${detail}`, { cause: { issues: result.issues } })
  }

  return result.value
};

/**
 * Get all data
 * 
 * GET /all_participants
 */
export const getApiAllParticipants = async (options?: GetApiAllParticipantsOptions) => {
const {baseUrl = "https://www.personalgenomes.org.uk/api/v1.3", fetch: fetchFn = fetch} = options ?? {}

const query = new URLSearchParams()
const headers = new Headers()
headers.set('accept', "application/json")

const url = `${baseUrl.replace(/\/+$/, '')}/all_participants${query.size > 0 ? `?${query}` : ''}`

const res = await fetchFn(url, {method: "GET", headers})

if (!res.ok) throw new Error(`Request failed with status ${res.status}`, {cause: {status: res.status, body: await res.text()}})

return validateResponse(getApiAllParticipantsResponse, await res.json())
};