Merge pull request #396 from cidgoh/grdi-6.2.1

update to grdi schema

package.json

@@ -1,6 +1,6 @@
 {
   "name": "data-harmonizer",
-  "version": "1.4.9",
+  "version": "1.4.10",
   "description": "A standardized spreadsheet editor and validator that can be run offline and locally",
   "repository": "git@github.com:cidgoh/DataHarmonizer.git",
   "license": "MIT",

script/tabular_to_schema.py

@@ -46,7 +46,7 @@
 
 		# Cleanup of cell contents.
 		for field in row:
-			if field != None:
+			if field != None and field != '':
 				row[field] = row[field].strip();
 
 		# A row may set a list of new class names to cycle through, which remain 
@@ -292,11 +292,11 @@
 			if row.get('meaning','') > '':
 				choice['meaning'] = row.get('meaning');
 
-			# At moment linkml doesn't support exact_mappings on 
+			# Export mappings can be established for any enumeration items too.
 			if len(EXPORT_FORMAT) > 0:
 				mappings = []
 				for export_field in EXPORT_FORMAT:
-					if row[export_field] > '':
+					if export_field in row and row[export_field] > '':
 						prefix = export_field[7:] + ':'
 						for value in row[export_field].split(';'):
 							mappings.append(prefix + value)

web/templates/grdi/export.js

@@ -1,2 +1,107 @@
-// A dictionary of possible export formats
-export default {};
+// Adds existing functions/methods to DataHarminizer.
+export default {
+  /**
+   * Download secondary headers and grid data.
+   * @param {String} baseName Basename of downloaded file.
+   * @param {Object} hot Handonstable grid instance.
+   * @param {Object} data See `data.js`.
+   * @param {Object} xlsx SheetJS variable.
+   */
+
+  BioSample: {
+    fileType: 'xls',
+    status: 'published',
+    method: function (dh) {
+      // Create an export table with template's headers (2nd row) and remaining rows of data
+      const ExportHeaders = new Map([
+        ['sample_name', []], 					// *
+		['bioproject_accession',[]],			// *
+//		['attribute_package',[]],				
+//		['GISAID_accession',[]],
+//		['GISAID_virus_name',[]],
+//		['collection_date',[]],
+		['collected_by', []],					// *
+		['sequenced_by',       []],		 		// *`
+//		['sequence_submitted_by', []],
+
+		['sample collection date',[]],		// *
+
+        [										// *
+          'geo_loc_name',
+          ['geo_loc_name (country)', 'geo_loc_name (state/province/region)', 'geo_loc_name (site)'],
+        ],
+        ['organism', []],
+//        ['isolate', []],
+        [
+          'isolation_source',
+          [
+            'anatomical_material',
+            'anatomical_part',
+            'body_product',
+            'environmental_material',
+            'environmental_site',
+            'collection_device',
+            'collection_method',
+            'food_product',
+            'food_product_properties',
+            'food_packaging'
+          ],
+        ],
+        ['anatomical_material', []],
+        ['anatomical_part', []],
+        ['body_product', []],
+        ['environmental_material', []],
+        ['environmental_site', []],
+        ['collection_device', []],
+        ['collection_method', []],
+//        ['lab_host', []],
+//        ['passage_history', []],
+//        ['passage_method', []],
+        ['host', []],							// *
+        ['host_disease', []],					// *
+//        ['host_health_state', []],
+//        ['host_disease_outcome', []],
+//        ['host_age', []],
+//        ['host_age_unit',   []],	
+//				['host_age_bin',   []],	
+//        ['host_sex', []],
+//        ['host_subject_id', []],
+        ['purpose_of_sampling',[]],				// *
+        ['purpose_of_sequencing', []],			// *
+//      ['gene_name_1', []],
+//      ['diagnostic_PCR_CT_value_1', []],
+//      ['gene_name_2', []],
+//      ['diagnostic_PCR_CT_value_2', []],
+//      ['description',[]],
+      ]);
+
+      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');
+
+      // 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) {
+          // Otherwise apply source (many to one) to target field transform:
+          const value = dh.getMappedField(
+            headerName,
+            inputRow,
+            sources,
+            sourceFields,
+            sourceFieldNameMap,
+            ':',
+            'BIOSAMPLE'
+          );
+          outputRow.push(value);
+        }
+        outputMatrix.push(outputRow);
+      }
+
+      return outputMatrix;
+    },
+  },
+};