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Use getMappedField
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* Need to update enums
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@ivansg44
ivansg44 committed Oct 3, 2024
1 parent a73a74a commit 6d82f5f
Showing 1 changed file with 73 additions and 66 deletions.
139 changes: 73 additions & 66 deletions web/templates/grdi/export.js
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Original file line number Diff line number Diff line change
Expand Up @@ -561,70 +561,70 @@ export default {
];
const longHeadersArr = Array.from(ExportHeaders.keys()).slice(2);
const GRDItoNCBIObj = {
'resistance_phenotype': {
'Resistant antimicrobial phenotype [ARO:3004301]':
'resistant',
'Susceptible antimicrobial phenotype [ARO:3004302]':
'susceptible',
'Intermediate antimicrobial phenotype [ARO:3004300]':
'intermediate',
'Nonsusceptible antimicrobial phenotype [ARO:3004303]':
'nonsusceptible',
'Antibiotic resistance not defined [GENEPIO:0002040]':
'not defined',
'Susceptible dose dependent antimicrobial phenotype [ARO:3004304]':
'susceptible-dose dependent'
},
'measurement_sign': {
'less than (<) [GENEPIO:0001002]': '<',
'less than or equal to (<=) [GENEPIO:0001003]': '<=',
'equal to (==) [GENEPIO:0001004]': '==',
'greater than (>) [GENEPIO:0001006]': '>',
'greater than or equal to (>=) [GENEPIO:0001005]': '>='
},
'measurement_units': {
'milligram per litre (mg/L) [UO:0000273]': 'mg/L',
'millimetre (mm) [UO:0000016]': 'mm'
},
'laboratory_typing_method': {
'Agar dilution [ARO:3004411]': 'agar dilution',
'Agar diffusion [NCIT:85595]': 'disk diffusion',
'Missing [GENEPIO:0001618]': 'missing'
},
'laboratory_typing_platform': {
'Microscan [ARO:3004400]': 'Microscan',
'Phoenix [ARO:3004401]': 'Phoenix',
'Sensititre [ARO:3004402]': 'Sensititre',
'Vitek System [ARO:3004403]': 'Vitek'
},
'vendor': {
'Becton Dickinson [ARO:3004405]': 'Becton Dickinson',
'bioMérieux [ARO:3004406]': 'Biomérieux',
'Siemens [ARO:3004407]': 'Siemens',
'Trek [ARO:3004409]': 'Trek'
},
'testing_standard': {
'British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]':
'BSAC',
'Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]':
'CLSI',
'Deutsches Institut für Normung (DIN) [ARO:3004367]':
'DIN',
'European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]':
'EUCAST',
'National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]':
'NARMS',
'National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]':
'NCCLS',
'Société Française de Microbiologie (SFM) [ARO:3004369]':
'SFM',
'Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]':
'SIR',
'Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]':
'WRG',
'Missing [GENEPIO:0001618]':
'missing'
}
// 'resistance_phenotype': {
// 'Resistant antimicrobial phenotype [ARO:3004301]':
// 'resistant',
// 'Susceptible antimicrobial phenotype [ARO:3004302]':
// 'susceptible',
// 'Intermediate antimicrobial phenotype [ARO:3004300]':
// 'intermediate',
// 'Nonsusceptible antimicrobial phenotype [ARO:3004303]':
// 'nonsusceptible',
// 'Antibiotic resistance not defined [GENEPIO:0002040]':
// 'not defined',
// 'Susceptible dose dependent antimicrobial phenotype [ARO:3004304]':
// 'susceptible-dose dependent'
// },
// 'measurement_sign': {
// 'less than (<) [GENEPIO:0001002]': '<',
// 'less than or equal to (<=) [GENEPIO:0001003]': '<=',
// 'equal to (==) [GENEPIO:0001004]': '==',
// 'greater than (>) [GENEPIO:0001006]': '>',
// 'greater than or equal to (>=) [GENEPIO:0001005]': '>='
// },
// 'measurement_units': {
// 'milligram per litre (mg/L) [UO:0000273]': 'mg/L',
// 'millimetre (mm) [UO:0000016]': 'mm'
// },
// 'laboratory_typing_method': {
// 'Agar dilution [ARO:3004411]': 'agar dilution',
// 'Agar diffusion [NCIT:85595]': 'disk diffusion',
// 'Missing [GENEPIO:0001618]': 'missing'
// },
// 'laboratory_typing_platform': {
// 'Microscan [ARO:3004400]': 'Microscan',
// 'Phoenix [ARO:3004401]': 'Phoenix',
// 'Sensititre [ARO:3004402]': 'Sensititre',
// 'Vitek System [ARO:3004403]': 'Vitek'
// },
// 'vendor': {
// 'Becton Dickinson [ARO:3004405]': 'Becton Dickinson',
// 'bioMérieux [ARO:3004406]': 'Biomérieux',
// 'Siemens [ARO:3004407]': 'Siemens',
// 'Trek [ARO:3004409]': 'Trek'
// },
// 'testing_standard': {
// 'British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]':
// 'BSAC',
// 'Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]':
// 'CLSI',
// 'Deutsches Institut für Normung (DIN) [ARO:3004367]':
// 'DIN',
// 'European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]':
// 'EUCAST',
// 'National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]':
// 'NARMS',
// 'National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]':
// 'NCCLS',
// 'Société Française de Microbiologie (SFM) [ARO:3004369]':
// 'SFM',
// 'Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]':
// 'SIR',
// 'Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]':
// 'WRG',
// 'Missing [GENEPIO:0001618]':
// 'missing'
// }
}

const sourceFields = dh.getFields(dh.table);
Expand Down Expand Up @@ -653,8 +653,15 @@ export default {
for (const [i, longHeader] of longHeadersArr.entries()) {
let wideHeader = antibiotic.concat('_', longHeader);
if (longHeader === 'vendor') wideHeader += '_name';
let wideVal =
inputRow[sourceFieldNameMap[wideHeader.replaceAll('-', '')]];
let wideVal = dh.getMappedField(
longHeader,
inputRow,
[wideHeader.replaceAll('-', '')],
sourceFields,
sourceFieldNameMap,
':',
'NCBI_ANTIBIOGRAM'
);
if (wideVal) {
atLeastOneWideVal = true;
if (longHeader in GRDItoNCBIObj) {
Expand Down

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