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Merge pull request #133 from ssi-dk/feat/add-new-field-mappings
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feat: add additional fields to aggregation pipeline
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@sjkp
sjkp authored Dec 20, 2024
2 parents d72eee6 + 6951ee9 commit 3f580f9
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Showing 9 changed files with 1,552 additions and 343 deletions.
9 changes: 3 additions & 6 deletions app/src/app/i18n.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -149,19 +149,16 @@ const fieldDisplayNames = {
qc_db_id: "QC_DB_ID",
qc_db_id2: "QC_DB_ID2",
qc_failed_tests: "QC_failed_tests",
qc_cgmlst_percent: "QC_cgMLST%",
cgmlst_schema_salmonella: "cgMLST skema Salmonella",
cgmlst_schema_ecoli: "cgMLST skema E. coli",
cgmlst_schema_campylobacter: "cgMLST skema Campylobacter",
cgmlst_schema_listeria: "cgMLST skema Listeria",
cgmlst_schema_klebsiella: "cgMLST skema Klebsiella",
call_percent: "Call_percent",
cgmlst_schema: "cgMLST skema",
trst: "TRST",
tcda: "tcdA",
tcdb: "tcdB",
cdta_cdtb: "cdtA_cdtB",
del_117: "117del",
a117t: "A117T",
cdiff_details: "Cdiff_details",
adhaesion: "Adhæsion",
} as { [key in keyof AnalysisResult]: string },
};

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170 changes: 141 additions & 29 deletions app/src/sap-client/models/AnalysisResultAllOf.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,13 @@ export interface AnalysisResultAllOf {
* @type {number}
* @memberof AnalysisResultAllOf
*/
qc_cgmlst_percent?: number;
call_percent?: number;
/**
*
* @type {number}
* @memberof AnalysisResultAllOf
*/
multiple_alleles?: number;
/**
*
* @type {string}
Expand Down Expand Up @@ -554,73 +560,151 @@ export interface AnalysisResultAllOf {
* @type {object}
* @memberof AnalysisResultAllOf
*/
cgmlst_schema_salmonella?: object;
cgmlst_schema?: object;
/**
*
* @type {object}
* @type {string}
* @memberof AnalysisResultAllOf
*/
cgmlst_schema_ecoli?: object;
trst?: string;
/**
*
* @type {object}
* @type {string}
* @memberof AnalysisResultAllOf
*/
cgmlst_schema_campylobacter?: object;
tcda?: string;
/**
*
* @type {object}
* @type {string}
* @memberof AnalysisResultAllOf
*/
cgmlst_schema_listeria?: object;
tcdb?: string;
/**
*
* @type {object}
* @type {string}
* @memberof AnalysisResultAllOf
*/
cgmlst_schema_klebsiella?: object;
cdta_cdtb?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
trst?: string;
del_117?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
tcda?: string;
a117t?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
tcdb?: string;
cdiff_details?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
cdta_cdtb?: string;
adhaesion?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
del_117?: string;
toxin?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
a117t?: string;
toxin_details?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
cdiff_details?: string;
bifrost_min_read_check?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_whats_my_species?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_assemblatron?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_assembly_qc?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_ssi_stamper?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_cge_mlst?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_cge_resfinder?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_seqsero?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_enterobase?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_salmonella_subspecies_dtartrate?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_chewbbaca?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_sp_ecoli?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_sp_cdiff?: string;
/**
*
* @type {string}
* @memberof AnalysisResultAllOf
*/
bifrost_amrfinderplus?: string;
}

export function AnalysisResultAllOfFromJSON(json: any): AnalysisResultAllOf {
Expand Down Expand Up @@ -651,7 +735,8 @@ export function AnalysisResultAllOfFromJSON(json: any): AnalysisResultAllOf {
'qc_db_id': !exists(json, 'qc_db_id') ? undefined : json['qc_db_id'],
'qc_db_id2': !exists(json, 'qc_db_id2') ? undefined : json['qc_db_id2'],
'qc_failed_tests': !exists(json, 'qc_failed_tests') ? undefined : (json['qc_failed_tests'] as Array<any>).map(AnalysisResultAllOfQcFailedTestsFromJSON),
'qc_cgmlst_percent': !exists(json, 'qc_cgmlst_percent') ? undefined : json['qc_cgmlst_percent'],
'call_percent': !exists(json, 'call_percent') ? undefined : json['call_percent'],
'multiple_alleles': !exists(json, 'multiple_alleles') ? undefined : json['multiple_alleles'],
'subspecies': !exists(json, 'subspecies') ? undefined : json['subspecies'],
'species_final': !exists(json, 'species_final') ? undefined : json['species_final'],
'st': !exists(json, 'st') ? undefined : json['st'],
Expand Down Expand Up @@ -712,18 +797,31 @@ export function AnalysisResultAllOfFromJSON(json: any): AnalysisResultAllOf {
'amr_tgc': !exists(json, 'amr_tgc') ? undefined : ResistanceFromJSON(json['amr_tgc']),
'amr_tmp': !exists(json, 'amr_tmp') ? undefined : ResistanceFromJSON(json['amr_tmp']),
'amr_van': !exists(json, 'amr_van') ? undefined : ResistanceFromJSON(json['amr_van']),
'cgmlst_schema_salmonella': !exists(json, 'cgmlst_schema_salmonella') ? undefined : json['cgmlst_schema_salmonella'],
'cgmlst_schema_ecoli': !exists(json, 'cgmlst_schema_ecoli') ? undefined : json['cgmlst_schema_ecoli'],
'cgmlst_schema_campylobacter': !exists(json, 'cgmlst_schema_campylobacter') ? undefined : json['cgmlst_schema_campylobacter'],
'cgmlst_schema_listeria': !exists(json, 'cgmlst_schema_listeria') ? undefined : json['cgmlst_schema_listeria'],
'cgmlst_schema_klebsiella': !exists(json, 'cgmlst_schema_klebsiella') ? undefined : json['cgmlst_schema_klebsiella'],
'cgmlst_schema': !exists(json, 'cgmlst_schema') ? undefined : json['cgmlst_schema'],
'trst': !exists(json, 'trst') ? undefined : json['trst'],
'tcda': !exists(json, 'tcda') ? undefined : json['tcda'],
'tcdb': !exists(json, 'tcdb') ? undefined : json['tcdb'],
'cdta_cdtb': !exists(json, 'cdta_cdtb') ? undefined : json['cdta_cdtb'],
'del_117': !exists(json, 'del_117') ? undefined : json['del_117'],
'a117t': !exists(json, 'a117t') ? undefined : json['a117t'],
'cdiff_details': !exists(json, 'cdiff_details') ? undefined : json['cdiff_details'],
'adhaesion': !exists(json, 'adhaesion') ? undefined : json['adhaesion'],
'toxin': !exists(json, 'toxin') ? undefined : json['toxin'],
'toxin_details': !exists(json, 'toxin_details') ? undefined : json['toxin_details'],
'bifrost_min_read_check': !exists(json, 'bifrost_min_read_check') ? undefined : json['bifrost_min_read_check'],
'bifrost_whats_my_species': !exists(json, 'bifrost_whats_my_species') ? undefined : json['bifrost_whats_my_species'],
'bifrost_assemblatron': !exists(json, 'bifrost_assemblatron') ? undefined : json['bifrost_assemblatron'],
'bifrost_assembly_qc': !exists(json, 'bifrost_assembly_qc') ? undefined : json['bifrost_assembly_qc'],
'bifrost_ssi_stamper': !exists(json, 'bifrost_ssi_stamper') ? undefined : json['bifrost_ssi_stamper'],
'bifrost_cge_mlst': !exists(json, 'bifrost_cge_mlst') ? undefined : json['bifrost_cge_mlst'],
'bifrost_cge_resfinder': !exists(json, 'bifrost_cge_resfinder') ? undefined : json['bifrost_cge_resfinder'],
'bifrost_seqsero': !exists(json, 'bifrost_seqsero') ? undefined : json['bifrost_seqsero'],
'bifrost_enterobase': !exists(json, 'bifrost_enterobase') ? undefined : json['bifrost_enterobase'],
'bifrost_salmonella_subspecies_dtartrate': !exists(json, 'bifrost_salmonella_subspecies_dtartrate') ? undefined : json['bifrost_salmonella_subspecies_dtartrate'],
'bifrost_chewbbaca': !exists(json, 'bifrost_chewbbaca') ? undefined : json['bifrost_chewbbaca'],
'bifrost_sp_ecoli': !exists(json, 'bifrost_sp_ecoli') ? undefined : json['bifrost_sp_ecoli'],
'bifrost_sp_cdiff': !exists(json, 'bifrost_sp_cdiff') ? undefined : json['bifrost_sp_cdiff'],
'bifrost_amrfinderplus': !exists(json, 'bifrost_amrfinderplus') ? undefined : json['bifrost_amrfinderplus'],
};
}

Expand Down Expand Up @@ -758,7 +856,8 @@ export function AnalysisResultAllOfToJSON(value?: AnalysisResultAllOf): any {
'qc_db_id': value.qc_db_id,
'qc_db_id2': value.qc_db_id2,
'qc_failed_tests': value.qc_failed_tests === undefined ? undefined : (value.qc_failed_tests as Array<any>).map(AnalysisResultAllOfQcFailedTestsToJSON),
'qc_cgmlst_percent': value.qc_cgmlst_percent,
'call_percent': value.call_percent,
'multiple_alleles': value.multiple_alleles,
'subspecies': value.subspecies,
'species_final': value.species_final,
'st': value.st,
Expand Down Expand Up @@ -819,18 +918,31 @@ export function AnalysisResultAllOfToJSON(value?: AnalysisResultAllOf): any {
'amr_tgc': ResistanceToJSON(value.amr_tgc),
'amr_tmp': ResistanceToJSON(value.amr_tmp),
'amr_van': ResistanceToJSON(value.amr_van),
'cgmlst_schema_salmonella': value.cgmlst_schema_salmonella,
'cgmlst_schema_ecoli': value.cgmlst_schema_ecoli,
'cgmlst_schema_campylobacter': value.cgmlst_schema_campylobacter,
'cgmlst_schema_listeria': value.cgmlst_schema_listeria,
'cgmlst_schema_klebsiella': value.cgmlst_schema_klebsiella,
'cgmlst_schema': value.cgmlst_schema,
'trst': value.trst,
'tcda': value.tcda,
'tcdb': value.tcdb,
'cdta_cdtb': value.cdta_cdtb,
'del_117': value.del_117,
'a117t': value.a117t,
'cdiff_details': value.cdiff_details,
'adhaesion': value.adhaesion,
'toxin': value.toxin,
'toxin_details': value.toxin_details,
'bifrost_min_read_check': value.bifrost_min_read_check,
'bifrost_whats_my_species': value.bifrost_whats_my_species,
'bifrost_assemblatron': value.bifrost_assemblatron,
'bifrost_assembly_qc': value.bifrost_assembly_qc,
'bifrost_ssi_stamper': value.bifrost_ssi_stamper,
'bifrost_cge_mlst': value.bifrost_cge_mlst,
'bifrost_cge_resfinder': value.bifrost_cge_resfinder,
'bifrost_seqsero': value.bifrost_seqsero,
'bifrost_enterobase': value.bifrost_enterobase,
'bifrost_salmonella_subspecies_dtartrate': value.bifrost_salmonella_subspecies_dtartrate,
'bifrost_chewbbaca': value.bifrost_chewbbaca,
'bifrost_sp_ecoli': value.bifrost_sp_ecoli,
'bifrost_sp_cdiff': value.bifrost_sp_cdiff,
'bifrost_amrfinderplus': value.bifrost_amrfinderplus,
};
}

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