[BI-1803] - Excel formatting preventing ontology file import

src/main/java/org/breedinginsight/services/parsers/excel/ExcelParser.java

@@ -87,11 +87,24 @@ public static List<ExcelRecord> parse(Sheet sheet, Set<String> columns) throws P
                 throw new ParsingException(ParsingExceptionType.EMPTY_ROW);
             }
 
+            // Flag for empty rows; for CSV, empty cells are empty string ("") rather than null.
+            boolean emptyRow = true;
             for(int colIndex=0; colIndex<row.getLastCellNum(); colIndex++) {
                 Cell cell = row.getCell(colIndex);
+                if (cell != null && cell.toString().length() > 0)
+                {
+                    // There is at least one value in this row, set emptyRow flag false.
+                    emptyRow = false;
+                }
                 data.put(indexColNameMap.get(colIndex), cell);
             }
 
+            // If the row has no cells with values, skip it.
+            if (data.isEmpty() || emptyRow)
+            {
+                continue;
+            }
+
             records.add(new ExcelRecord(data));
 
         }

src/test/java/org/breedinginsight/services/parsers/TraitFileParserUnitTest.java

@@ -334,4 +334,33 @@ void parseXlsxMultipleRowsSuccess() {
         assertEquals(3, traits.size(), "number of traits different than expected");
     }
 
+    @Test
+    @SneakyThrows
+    void parseCsvNullRowsSuccess() {
+        File file = new File("src/test/resources/files/ontology/ontology_null_rows.csv");
+        InputStream inputStream = new FileInputStream(file);
+        List<Trait> traits = parser.parseCsv(inputStream);
+
+        assertEquals(3, traits.size(), "number of traits different than expected");
+    }
+
+    @Test
+    @SneakyThrows
+    void parseXlsNullRowsSuccess() {
+        File file = new File("src/test/resources/files/ontology/ontology_null_rows.xls");
+        InputStream inputStream = new FileInputStream(file);
+        List<Trait> traits = parser.parseExcel(inputStream);
+
+        assertEquals(3, traits.size(), "number of traits different than expected");
+    }
+
+    @Test
+    @SneakyThrows
+    void parseXlsxNullRowsSuccess() {
+        File file = new File("src/test/resources/files/ontology/ontology_null_rows.xlsx");
+        InputStream inputStream = new FileInputStream(file);
+        List<Trait> traits = parser.parseExcel(inputStream);
+
+        assertEquals(3, traits.size(), "number of traits different than expected");
+    }
 }

src/test/resources/files/ontology/ontology_null_rows.csv

@@ -0,0 +1,8 @@
+Name,Full Name,Term Type,Description,Synonyms,Status,Tags,Trait Entity,Trait Attribute,Method Description,Method Class,Method Formula,Scale Class,Units,Scale Decimal Places,Scale Lower Limit,Scale Upper Limit,Scale Categories
+Pheno 1,,,Pheno 1,,,,Pheno,1,,Measurement,,Numerical,cm,,,,
+Pheno 2,,,Pheno 2,,,,Pheno,2,,Measurement,,Numerical,ug/ml,,,,
+Pheno 3,,,Pheno 3,,,,Pheno,3,,Observation,,Date,,,,,
+,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,