Merge pull request #233 from cidgoh/vocabulary-update

Vocabulary update
cidgoh · Nov 9, 2021 · f663164 · f663164
2 parents 8cd7f40 + 6bd2472
commit f663164
Showing 1 changed file with 53 additions and 14 deletions.
diff --git a/template/canada_covid19/export.js b/template/canada_covid19/export.js
@@ -66,6 +66,18 @@ var exportVirusSeq_Portal = (baseName, hot, data, xlsx, fileType) => {
     ['restricted access', 'Restricted Access']
   ]);
 
+  studyMap = {
+    'Alberta Precision Labs (APL)': 'ABPL-AB',
+    'BCCDC Public Health Laboratory': 'BCCDC-BC',
+    'Manitoba Cadham Provincial Laboratory': 'MCPL-MB',
+    'New Brunswick - Vitalité Health Network': 'VHN-NB',
+    'Newfoundland and Labrador - Eastern Health': 'EH-NL',
+    'Nova Scotia Health Authority': 'NSHA-NS',
+    'Public Health Ontario (PHO)': 'PHO-ON',
+    'Laboratoire de santé publique du Québec (LSPQ)': 'LSPQ-QC',
+    'Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)': 'RRPL-SK',
+  }
+
   const sourceFields = getFields(data);
   const sourceFieldNameMap = getFieldNameMap(sourceFields);
   // Fills in the above mapping (or just set manually above) 
@@ -74,6 +86,7 @@ var exportVirusSeq_Portal = (baseName, hot, data, xlsx, fileType) => {
   // Copy headers to 1st row of new export table
   const outputMatrix = [[...ExportHeaders.keys()]];
 
+  const numeric_datatypes = new Set(['xs:nonNegativeInteger', 'xs:decimal']);
 
   for (const inputRow of getTrimmedData(hot)) {
     const outputRow = [];
@@ -86,7 +99,19 @@ var exportVirusSeq_Portal = (baseName, hot, data, xlsx, fileType) => {
         // Otherwise apply source (many to one) to target field transform:
         var value = getMappedField(headerName, inputRow, sources, sourceFields, sourceFieldNameMap, ':', 'VirusSeq_Portal');
 
-        const numeric_datatypes = new Set(['xs:nonNegativeInteger', 'xs:decimal']);
+        if (headerName == 'study_id') {
+
+          // Autopopulate study_id based on studyMap
+          const lab = inputRow[sourceFieldNameMap['sequence submitted by']];     
+          if (lab && lab in studyMap) {
+            value = studyMap[lab];
+          }
+        }
+
+        // Add % to breadth of coverage since required.
+        if (headerName == 'breadth of coverage value' && value && value.length && value.substr(-1) != '%') {
+          value = value + '%';
+        }
 
         // Some columns have an extra ' null reason' field for demultiplexing null value into.
         if (ExportHeaders.has(headerName + ' null reason')) {
@@ -627,16 +652,13 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => {
   // Copy headers to 1st row of new export table
   const outputMatrix = [[...ExportHeaders.keys()]];
 
-  // Conversion of all cancogen metadata keywords to NML LIMS version
-  /*
   nullOptionsMap = new Map([
-    ['Not Applicable', 'NA'],
-    ['Missing', 'MISSING'],
-    ['Not Collected', 'NOT_COLLECTED'],
-    ['Not Provided', 'NOT_PROVIDED'],
-    ['Restricted Access', 'RESTRICTED_ACCESS']
+    ['not applicable', 'Not Applicable'],
+    ['missing', 'Missing'],
+    ['not collected', 'Not Collected'],
+    ['not provided', 'Not Provided'],
+    ['restricted access', 'Restricted Access']
   ]);
-  */
 
   for (const inputRow of getTrimmedData(hot)) {
     const outputRow = [];
@@ -660,9 +682,9 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => {
       // Handle granularity of "HC_COLLECT_DATE"
       // by looking at year or month in "sample collection date precision"
       if (headerName === 'HC_COLLECT_DATE') {
-        const value = inputRow[sourceFieldNameMap['sample collection date']] || '';
+        let value = inputRow[sourceFieldNameMap['sample collection date']] || '';
+        value = fixNullOptionCase(value,nullOptionsMap);
         const date_unit = inputRow[sourceFieldNameMap['sample collection date precision']];
-
         outputRow.push(setDateChange(date_unit, value, '01'));
         continue;
       }
@@ -685,7 +707,7 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => {
           }
           if (fieldName === 'host (scientific name)' || fieldName === 'host (common name)') {
             if (value === 'Homo sapiens' || value === 'Human')
-              cellValue = 'HUMAN'
+              cellValue = 'Human'
             else
               cellValue = 'ANIMAL'
             break;
@@ -700,8 +722,8 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => {
       }
 
       // Otherwise apply source (many to one) to target field transform:
-      const value = getMappedField(headerName, inputRow, sources, sourceFields, sourceFieldNameMap, ';', 'NML_LIMS');
-
+      let value = getMappedField(headerName, inputRow, sources, sourceFields, sourceFieldNameMap, ';', 'NML_LIMS');
+      value = fixNullOptionCase(value, nullOptionsMap);
       outputRow.push(value);
     }
     outputMatrix.push(outputRow);
@@ -720,3 +742,20 @@ var EXPORT_FORMATS = {
 
 };
 
+/**
+ * If given value is a null value, normalize its capitalization
+ * @param {String} value to check.
+ * @param {Object} nullOptionsMap dictionary of null values.
+ * @return {String} value
+ */
+var fixNullOptionCase = (value, nullOptionsMap) => {
+  if (value) {
+    const valuelc = value.toLowerCase();
+    if (nullOptionsMap.has(valuelc)) {
+      const value2 = nullOptionsMap.get(valuelc);
+      if (value != value2)
+        value = value2;
+    }
+  }
+  return value;
+}