import {z} from 'zod'

export type V2VirusTableField = 'unspecified' | 'nucleotide_accession' | 'species_tax_id' | 'species_name' | 'genus' | 'family' | 'nucleotide_length' | 'isolate_name' | 'sequence_type' | 'nuc_completeness' | 'geo_location' | 'us_state' | 'host_name' | 'host_tax_id' | 'collection_date' | 'bioproject' | 'biosample' | 'polyprotein_name' | 'protein_name' | 'protein_accession' | 'protein_synonym' | 'cds_span';

export type V2ViralSequenceType = 'GENOME' | 'CDS' | 'PROTEIN' | 'NONE';

export type V2VirusDatasetReportType = 'DATASET_REPORT' | 'ANNOTATION' | 'BIOSAMPLE_REPORT';

export type V2TableFormat = 'tsv' | 'csv' | 'jsonl';

export type V2Sars2ProteinDatasetRequest = {proteins?: Array<string> | undefined, refseq_only?: boolean | undefined, annotated_only?: boolean | undefined, released_since?: string | undefined, updated_since?: string | undefined, host?: string | undefined, pangolin_classification?: string | undefined, geo_location?: string | undefined, usa_state?: string | undefined, complete_only?: boolean | undefined, table_fields?: Array<V2VirusTableField> | undefined, include_sequence?: Array<V2ViralSequenceType> | undefined, aux_report?: Array<V2VirusDatasetReportType> | undefined, format?: V2TableFormat | undefined};

export type CreateApiVirusTaxonSars2ProteinArgs = {body: V2Sars2ProteinDatasetRequest};

export type CreateApiVirusTaxonSars2ProteinOptions = {baseUrl?: string | undefined, ApiKeyAuthHeader?: string | undefined, fetch?: typeof fetch | undefined};

export const v2DownloadSummaryHydrated = z.object({estimated_file_size_mb: z.number().int().optional(), url: z.string().optional(), cli_download_command_line: z.string().optional()});

export const v2DownloadSummaryDehydrated = z.object({estimated_file_size_mb: z.number().int().optional(), url: z.string().optional(), cli_download_command_line: z.string().optional(), cli_rehydrate_command_line: z.string().optional()});

export const v2reportsErrorAssemblyErrorCode = z.enum(["UNKNOWN_ASSEMBLY_ERROR_CODE", "INVALID_BIOPROJECT_IDS", "NO_ASSEMBLIES_FOR_BIOPROJECTS", "INVALID_TAXON", "MISSING_SEARCH_FIELD", "INVALID_BIOSAMPLE_IDS", "NO_ASSEMBLIES_FOR_BIOSAMPLE_IDS", "NO_ASSEMBLIES_FOR_ASSEMBLY_NAMES", "INVALID_WGS_ACCESSIONS", "NO_ASSEMBLIES_FOR_WGS_ACCESSIONS"]);

export const v2reportsErrorGeneErrorCode = z.enum(["UNKNOWN_GENE_ERROR_CODE", "INCOMPLETE_LOOKUP_SYMBOL", "INVALID_TAXON_GENE_ARGUMENT"]);

export const v2reportsErrorOrganelleErrorCode = z.enum(["UNKNOWN_ORGANELLE_ERROR_CODE", "INVALID_ORGANELLE_TAXON", "NO_ORGANELLES_FOR_ACCESSION"]);

export const v2reportsErrorVirusErrorCode = z.literal("UNKNOWN_VIRUS_ERROR_CODE");

export const v2reportsErrorTaxonomyErrorCode = z.enum(["UNKNOWN_TAXONOMY_ERROR_CODE", "INVALID_TAXONOMY_TAXON"]);

export const v2reportsErrorSequenceErrorCode = z.enum(["UNKNOWN_SEQUENCE_ERROR_CODE", "INVALID_SEQUENCE_ACCESSION"]);

export const v2reportsError = z.object({assembly_error_code: v2reportsErrorAssemblyErrorCode.optional(), gene_error_code: v2reportsErrorGeneErrorCode.optional(), organelle_error_code: v2reportsErrorOrganelleErrorCode.optional(), virus_error_code: v2reportsErrorVirusErrorCode.optional(), taxonomy_error_code: v2reportsErrorTaxonomyErrorCode.optional(), sequence_error_code: v2reportsErrorSequenceErrorCode.optional(), reason: z.string().optional(), message: z.string().optional(), invalid_identifiers: z.array(z.string()).optional()});

export const v2reportsWarningGeneWarningCode = z.enum(["UNKNOWN_GENE_WARNING_CODE", "ACCESSION_VERSION_MISMATCH", "REPLACED_GENE_ID", "DISCONTINUED_GENE_ID", "UNRECOGNIZED_GENE_ID", "UNRECOGNIZED_GENE_SYMBOL", "UNRECOGNIZED_ACCESSION", "UNRECOGNIZED_TAX_TOKEN", "NO_GENE_ANNOTATION_FOUND", "ABOVE_SPECIES_TAXON"]);

export const v2reportsWarningReplacedId = z.object({requested: z.string().optional(), returned: z.string().optional()});

export const v2reportsWarning = z.object({gene_warning_code: v2reportsWarningGeneWarningCode.optional(), reason: z.string().optional(), message: z.string().optional(), replaced_id: v2reportsWarningReplacedId.optional(), unrecognized_identifier: z.string().optional()});

export const v2reportsMessage = z.object({error: v2reportsError.optional(), warning: v2reportsWarning.optional()});

export const v2DownloadSummaryFileSummary = z.object({file_count: z.number().int().optional(), size_mb: z.number().optional()});

export const v2DownloadSummaryAvailableFiles = z.object({all_genomic_fasta: v2DownloadSummaryFileSummary.optional(), genome_gff: v2DownloadSummaryFileSummary.optional(), genome_gbff: v2DownloadSummaryFileSummary.optional(), rna_fasta: v2DownloadSummaryFileSummary.optional(), prot_fasta: v2DownloadSummaryFileSummary.optional(), genome_gtf: v2DownloadSummaryFileSummary.optional(), cds_fasta: v2DownloadSummaryFileSummary.optional(), sequence_report: v2DownloadSummaryFileSummary.optional(), annotation_report: v2DownloadSummaryFileSummary.optional()});

export const v2DownloadSummary = z.object({record_count: z.number().int().optional(), assembly_count: z.number().int().optional(), resource_updated_on: z.string().optional(), hydrated: v2DownloadSummaryHydrated.optional(), dehydrated: v2DownloadSummaryDehydrated.optional(), errors: z.array(v2reportsError).optional(), messages: z.array(v2reportsMessage).optional(), available_files: v2DownloadSummaryAvailableFiles.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 a download summary of a SARS-CoV-2 protein data package by protein name
 * 
 * POST /virus/taxon/sars2/protein
 */
export const createApiVirusTaxonSars2Protein = async (args: CreateApiVirusTaxonSars2ProteinArgs, options?: CreateApiVirusTaxonSars2ProteinOptions) => {
const {baseUrl = "https://api.ncbi.nlm.nih.gov/datasets/v2", fetch: fetchFn = fetch, ApiKeyAuthHeader} = options ?? {}

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

if (ApiKeyAuthHeader !== undefined) headers.set("api-key", ApiKeyAuthHeader)

const url = `${baseUrl.replace(/\/+$/, '')}/virus/taxon/sars2/protein${query.size > 0 ? `?${query}` : ''}`

const res = await fetchFn(url, {method: "POST", headers, body: JSON.stringify(args.body)})

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

return validateResponse(v2DownloadSummary, await res.json())
};