Merge branch 'master' into patch-2

requirements.txt

@@ -1,4 +1,4 @@
 # version requirement?
 dpath==2.0.6
 black
-linkml_runtime
+linkml-runtime

script/data-harmonizer/index.js

@@ -147,7 +147,10 @@ let DataHarmonizer = {
 			return template_name;
 		}
 		catch(err) {
-		  console.log(err);
+			console.log(err);
+			$('#missing-template-msg').text(`Unable to load template at path "${template_path}". Path should consist of [template folder name]/[template name] with correct capitalization.`);
+			$('#missing-template-modal').modal('show');
+			return false;
 		}
 
 	},

template/export.js

@@ -1,15 +1,38 @@
-
 // A list of the export functions keyed by the Export menu name they should appear as:
 var EXPORT_FORMATS = {
+  /*
+    Example_Format_Name: {
+    'fileType': 'xls', // or 'xlsx', 'tsv', 'csv'
+    'status': 'published', // or 'draft'
+    method: function (dh) {
+      // Conversion code
+      const ExportHeaders = new Map([
+        ['sample_name', [optional list of source fields to join values from; delimiter is usually semicolon]],
+        /// ... list of export table fields in order.
+      ])
 
-};
+      const sourceFields = dh.getFields(dh.table);
+      const sourceFieldNameMap = dh.getFieldNameMap(sourceFields);
+      // Fills in the above mapping (or just set manually above) 
+      dh.getHeaderMap(ExportHeaders, sourceFields, 'BIOSAMPLE');
 
-/*
-// Examples:
-var EXPORT_FORMATS = {
-  "IRIDA":        {'method': exportIRIDA, 'fileType': 'xls', 'status': 'published'},
-  "GISAID":       {'method': exportGISAID,'fileType': 'xls', 'status': 'published'},
-  "BioSample":    {'method': exportBioSample,'fileType': 'xls', 'status': 'published'},
-  "CNPHI LaSER":  {'method': exportLASER, 'fileType': 'csv (ASCII)', 'status': 'published'}
+      // Copy headers to 1st row of new export table
+      const outputMatrix = [[...ExportHeaders.keys()]];
+
+      for (const inputRow of dh.getTrimmedData(dh.hot)) {
+        const outputRow = [];
+        for (const [headerName, sources] of ExportHeaders) {
+
+          // Any custom rules here for data conversions
+          
+          // Otherwise apply source (many to one) to target field transform:
+          const value = dh.getMappedField(headerName, inputRow, sources, sourceFields,sourceFieldNameMap, ':', 'Example_Format_Name') 
+          outputRow.push(value);
+        }
+        outputMatrix.push(outputRow);
+      }
+
+      return outputMatrix
+    }
+  */
 };
-*/

template/monkeypox/export.js

@@ -262,7 +262,7 @@ var EXPORT_FORMATS = {
 				['PH_RELATED_RELATIONSHIP_TYPE', []],
 				['PH_ISOLATION_SITE_DESC',  []],
 				['PH_ISOLATION_SITE',       []],
-				//['PH_SPECIMEN_SOURCE',      []], // Calculated field (not in import)
+				['PH_SPECIMEN_SOURCE',      []], // Calculated field (not in import)
 				['PH_SPECIMEN_SOURCE_DESC', []],
 				//['PH_ENVIRONMENTAL_MATERIAL', []],
 				//['PH_ENVIRONMENTAL_SITE',   []],