Implement transformation of GRDI vals to NCBI

web/templates/grdi/export.js

@@ -560,6 +560,72 @@ export default {
         'trimethoprim-sulfamethoxazole'
       ];
       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'
+        }
+      }
 
       const sourceFields = dh.getFields(dh.table);
       const sourceFieldNameMap = dh.getFieldNameMap(sourceFields);
@@ -587,10 +653,15 @@ export default {
           for (const [i, longHeader] of longHeadersArr.entries()) {
             let wideHeader = antibiotic.concat('_', longHeader);
             if (longHeader === 'vendor') wideHeader += '_name';
-            const wideVal =
+            let wideVal =
               inputRow[sourceFieldNameMap[wideHeader]];
             if (wideVal) {
               atLeastOneWideVal = true;
+              if (longHeader in GRDItoNCBIObj) {
+                if (wideVal in GRDItoNCBIObj[longHeader]) {
+                  wideVal = GRDItoNCBIObj[longHeader][wideVal];
+                }
+              }
               longRow[i+2] = wideVal;
             }
           }