[BI-2883] - Add pedigree column to germplasm download files

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java

@@ -204,8 +204,7 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
                     germplasm.setAdditionalInfo(additionalInfo);
                 }
 
-                // TODO: BI-1883 to cleanup this workaround for the pedigree string
-                String pedigree = processBreedbasePedigree(germplasm.getPedigree());
+                String pedigree = germplasm.getPedigree();
                 additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE, pedigree);
 
                 String gidPedigreeString = "";
@@ -281,34 +280,6 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
         return programGermplasmMap;
     }
 
-    // TODO: hack for now, probably should update breedbase
-    // Made a JIRA card BI-1883 for this
-    // Breedbase will return NA/NA for no pedigree or NA/father, mother/NA
-    // strip NAs before saving RAW_PEDIGREE, if there was a germplasm with name NA it would be in format NA [program key]
-    // so that case should be ok if we just strip NA/NA, NA/, or /NA<\0>
-    private String processBreedbasePedigree(String pedigree) {
-
-        if (pedigree != null) {
-            if (pedigree.equals("NA/NA")) {
-                return "";
-            }
-
-            // Technically processGermplasmForDisplay should handle ok without stripping these NAs but will strip anyways
-            // for consistency.
-            // We only allow the /NA case for single parent as we require a female parent in the pedigree
-            // keep the leading slash, will be handled by processGermplasmForDisplay
-            if (pedigree.endsWith("/NA")) {
-                return pedigree.substring(0, pedigree.length()-2);
-            }
-
-            // shouldn't have this case in our data but just in case
-            if (pedigree.startsWith("NA/")) {
-                return pedigree.substring(2);
-            }
-        }
-        return pedigree;
-    }
-
     public List<BrAPIGermplasm> createBrAPIGermplasm(List<BrAPIGermplasm> postBrAPIGermplasmList, UUID programId, ImportUpload upload) {
         GermplasmApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), GermplasmApi.class);
         var program = programDAO.fetchOneById(programId);

src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java

@@ -177,6 +177,12 @@ public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm,
                 row.put("Synonyms", joinedSynonyms);
             }
 
+            // Pedigrees
+            if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME) != null) {
+                String pedigreeString = germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME).getAsString();
+                row.put("Pedigree", pedigreeString);
+            }
+
             processedData.add(row);
         }
         return processedData;

src/main/java/org/breedinginsight/services/parsers/germplasm/GermplasmFileColumns.java

@@ -28,6 +28,7 @@ public enum GermplasmFileColumns {
     NAME("Germplasm Name", Column.ColumnDataType.STRING),
     BREEDING_METHOD("Breeding Method", Column.ColumnDataType.STRING),
     SOURCE("Source", Column.ColumnDataType.STRING),
+    PEDIGREE("Pedigree", Column.ColumnDataType.STRING),
     FEMALE_PARENT_GID("Female Parent GID", Column.ColumnDataType.INTEGER),
     MALE_PARENT_GID("Male Parent GID", Column.ColumnDataType.INTEGER),
     ENTRY_NO("Entry No", Column.ColumnDataType.INTEGER),

src/test/java/org/breedinginsight/services/BrAPIGermplasmServiceUnitTest.java

@@ -171,8 +171,11 @@ public void getGermplasmListExport() {
         assertEquals(2, resultTable.rowCount(), "Wrong number of rows were exported");
         assertEquals("Germplasm A", resultTable.get(0, 1), "Incorrect data exported");
         // Check that "GID" column matches "Entry No" for both (https://breedinginsight.atlassian.net/browse/BI-2266).
-        assertEquals(resultTable.get(0, 0), resultTable.get(0, 6), "Incorrect data exported");
-        assertEquals(resultTable.get(1, 0), resultTable.get(1, 6), "Incorrect data exported");
+        assertEquals(resultTable.get(0, 0), resultTable.get(0, 7), "Incorrect data exported");
+        assertEquals(resultTable.get(1, 0), resultTable.get(1, 7), "Incorrect data exported");
+        //Assert "Pedigree" column contains properly formatted data
+        assertEquals(resultTable.get(0, 4), "", "Incorrect data exported");
+        assertEquals(resultTable.get(1, 4), "Germplasm A", "Incorrect data exported");
     }
 
     @Test