Updated orchard file generator module and sql to reduce duplicates, further streamline query, send shipped, and handle nulls.

Author: NIRC-IT

nirc_ehr/src/org/labkey/nirc_ehr/NIRCOrchardFileGenerator.java

@@ -121,7 +121,6 @@ public void run()
 
                 new TableSelector(ti, PageFlowUtil.set("Id", "gender", "birth", "species", "protocol", "PI", "Vet", "cage", "alive"), filter, null).forEachResults(rs -> {
                     sb.append("PID|1|");
-
                     sb.append(rs.getString("Id")).append("|");
                     sb.append(rs.getString("Id")).append("||");
                     sb.append(rs.getString("Id")).append("^").append(rs.getString("species")).append("||");
@@ -132,21 +131,21 @@ else if (Objects.equals(rs.getString("gender"), "3"))
                         sb.append("M");
                     else sb.append("U");
                     sb.append("||NHP|"); //build out if other than non-human primate
-                    sb.append(rs.getString("cage"));
+                    sb.append(rs.getString("cage") == null ? "" : rs.getString("cage"));
                     sb.append("^New Iberia^LA^70506|||||||||||");
                     sb.append(rs.getString("species")).append("|");
                     if (Objects.equals(rs.getString("alive"),"Shipped"))
                         sb.append("OFFSITE").append("|||||||");
                     else
-                        sb.append(rs.getString("protocol")).append("|||||||");
+                        sb.append(rs.getString("protocol") == null ? "" : rs.getString("protocol")).append("|||||||");
                     if (Objects.equals(rs.getString("alive"), "Alive"))
                         sb.append("N");
                     else
                         sb.append("Y");
                     sb.append(System.lineSeparator());
-                    sb.append("ZCP|Veterinarian|").append(rs.getString("Vet")).append("|");
+                    sb.append("ZCP|Veterinarian|").append(rs.getString("Vet") == null ? "" : rs.getString("Vet")).append("|");
                     sb.append(System.lineSeparator());
-                    sb.append("PD1||||").append(rs.getString("PI")).append("|");
+                    sb.append("PD1||||").append(rs.getString("PI") == null ? "" : rs.getString("PI")).append("|");
                     sb.append(System.lineSeparator());
                 });