import { MolecularProfile } from 'cbioportal-ts-api-client';

export const MOLECULAR_PROFILE_MUTATIONS_SUFFIX = '_mutations';
export const MOLECULAR_PROFILE_UNCALLED_MUTATIONS_SUFFIX = `${MOLECULAR_PROFILE_MUTATIONS_SUFFIX}_uncalled`;
export const MUTATION_STATUS_GERMLINE = 'Germline';

export const SAMPLE_CANCER_TYPE_UNKNOWN = 'Unknown';

/* cbioportal api request arguments */
export const enum REQUEST_ARG_ENUM {
    PROJECTION_META = 'META',
    PROJECTION_SUMMARY = 'SUMMARY',
    PROJECTION_DETAILED = 'DETAILED',
    CLINICAL_DATA_TYPE_PATIENT = 'PATIENT',
    CLINICAL_DATA_TYPE_SAMPLE = 'SAMPLE',
}

/* cbioportal api responses */

/* cbioportal api responses - general response values */
export const RESPONSE_VALUE_NA = 'NA';

/* cbioportal api responses - clinical attribute identifiers */
export const enum CLINICAL_ATTRIBUTE_ID_ENUM {
    CANCER_TYPE = 'CANCER_TYPE',
    CANCER_TYPE_DETAILED = 'CANCER_TYPE_DETAILED',
    ASCN_PURITY = 'ASCN_PURITY',
    ASCN_WGD = 'ASCN_WGD',
    MSI_SCORE = 'MSI_SCORE',
    MSI_TYPE = 'MSI_TYPE',
    TMB_SCORE = 'CVR_TMB_SCORE',
}

export const enum MIS_TYPE_VALUE {
    INSTABLE = 'Instable',
}

export const MSI_H_THRESHOLD = 10;
export const TMB_H_THRESHOLD = 10;

/* cbioportal api responses - clinical attribute fields and subfields */
export const enum CLINICAL_ATTRIBUTE_FIELD_ENUM {
    ID = 'clinicalAttributeId',
    DATATYPE_NUMBER = 'NUMBER',
    DATATYPE_STRING = 'STRING',
    DATATYPE_COUNTS_MAP = 'COUNTS_MAP',
}

/* cbioportal api responses - mutation data fields and subfields */
export const enum MUTATION_DATA_FIELD_ENUM {
    ASCN_INTEGER_COPY_NUMBER = 'ascnIntegerCopyNumber',
    TOTAL_COPY_NUMBER = 'totalCopyNumber',
    MINOR_COPY_NUMBER = 'minorCopyNumber',
    EXPECTED_ALT_COPIES = 'expectedAltCopies',
}

/* cbioportal api responses - genetic profile fields and subfields */
export const enum GENETIC_PROFILE_FIELD_ENUM {
    MOLECULAR_ALTERATION_TYPE = 'molecularAlterationType',
    STUDY_ID = 'studyId',
}

/* genome nexus api request arguments */
export const enum GENOME_NEXUS_ARG_FIELD_ENUM {
    ANNOTATION_SUMMARY = 'annotation_summary',
    HOTSPOTS = 'hotspots',
    MUTATION_ASSESSOR = 'mutation_assessor',
    MY_VARIANT_INFO = 'my_variant_info',
    SIGNAL = 'signal',
    CLINVAR = 'clinvar',
}

export const AlterationTypeText: {
    [K in MolecularProfile['molecularAlterationType']]: string;
} = {
    MUTATION_EXTENDED: 'mutations',
    COPY_NUMBER_ALTERATION: 'copy number alterations',
    MRNA_EXPRESSION: 'mRNA expression',
    PROTEIN_LEVEL: 'protein expression',
    STRUCTURAL_VARIANT: 'structural variants',
    GENERIC_ASSAY: 'generic assay',
    GENESET_SCORE: 'geneset score',
    METHYLATION: 'methylation',
    MICRO_RNA_EXPRESSION: 'micro rna expression',
    MRNA_EXPRESSION_NORMALS: 'MRNA expression normals',
    METHYLATION_BINARY: 'methylation binary',
    MUTATION_UNCALLED: 'mutation uncalled',
    PHOSPHORYLATION: 'phosphorylation',
    PROTEIN_ARRAY_PHOSPHORYLATION: 'protein array phosphorylation',
    PROTEIN_ARRAY_PROTEIN_LEVEL: 'protein array protein level',
    RNA_EXPRESSION: 'RNA expression',
};

// TODO: type this like the above so that it contains
// all possible keys (need to figure out FUSION first though, which is no longer a type)
// do we still need to support it?
export const AlterationTypeConstants = {
    MUTATION_EXTENDED: 'MUTATION_EXTENDED',
    COPY_NUMBER_ALTERATION: 'COPY_NUMBER_ALTERATION',
    MRNA_EXPRESSION: 'MRNA_EXPRESSION',
    PROTEIN_LEVEL: 'PROTEIN_LEVEL',
    STRUCTURAL_VARIANT: 'STRUCTURAL_VARIANT',
    FUSION: 'FUSION',
    GENERIC_ASSAY: 'GENERIC_ASSAY',
    GENESET_SCORE: 'GENESET_SCORE',
    METHYLATION: 'METHYLATION',
    MICRO_RNA_EXPRESSION: 'MICRO_RNA_EXPRESSION',
    MRNA_EXPRESSION_NORMALS: 'MRNA_EXPRESSION_NORMALS',
    METHYLATION_BINARY: 'METHYLATION_BINARY',
    MUTATION_UNCALLED: 'MUTATION_UNCALLED',
    PHOSPHORYLATION: 'PHOSPHORYLATION',
    PROTEIN_ARRAY_PHOSPHORYLATION: 'PROTEIN_ARRAY_PHOSPHORYLATION',
    PROTEIN_ARRAY_PROTEIN_LEVEL: 'PROTEIN_ARRAY_PROTEIN_LEVEL',
    RNA_EXPRESSION: 'RNA_EXPRESSION',
};

export const DataTypeConstants = {
    DISCRETE: 'DISCRETE',
    CONTINUOUS: 'CONTINUOUS',
    ZSCORE: 'Z-SCORE',
    MAF: 'MAF',
    LOGVALUE: 'LOG-VALUE',
    LOG2VALUE: 'LOG2-VALUE',
    FUSION: 'FUSION',
    SV: 'SV',
    LIMITVALUE: 'LIMIT-VALUE',
    BINARY: 'BINARY',
    CATEGORICAL: 'CATEGORICAL',
};