From f5c059840ae491511bc9f7bf0d7a1d1a7ad4edc0 Mon Sep 17 00:00:00 2001
From: =?utf8?q?Andreas=20M=C3=BCller?= <a.mueller@bgbm.org>
Date: Mon, 18 Jan 2016 10:23:52 +0100
Subject: [PATCH] Latest Cuba import developments

---
 .../etaxonomy/cdm/app/cuba/CubaActivator.java | 22 +++++++++----------
 .../cdm/io/cuba/CubaExcelImport.java          | 10 ++++-----
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java
index 96ee23a6..4ed48202 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java
@@ -41,31 +41,31 @@ public class CubaActivator {
 
 	boolean invers = true;
 	boolean include = !invers;
+	boolean exists = true;
 
     boolean doAsteraceae = include;
-    boolean doConvolvulaceae = include;
-    boolean doCyperaceae = ! include;
+    boolean doConvolvulaceae = include && exists;   //x
+    boolean doCyperaceae = include && exists;   //x
     boolean doDicotA_C = include;
     boolean doDicotD_M = include;
     boolean doDicotN_Z = include;
     boolean doEuphorbiaceae = include;
-    boolean doFabaceae = ! include;
+    boolean doFabaceae = include && exists;
     boolean doGymnospermae = include;
     boolean doLamVerbenaceae = include;
-    boolean doMalpighiaceae = ! include;
-    boolean doMelastomataceae = ! include;
-    boolean doMonocots = ! include ;
-    boolean doMyrtaceae = include;
+    boolean doMalpighiaceae = include && exists;
+    boolean doMelastomataceae = include && exists;
+    boolean doMonocots = include && exists;
+    boolean doMyrtaceae = ! include && exists;
     boolean doOrchidaceae = include;
     boolean doRubiaceae = include;
-    boolean doUrticaceae = ! include;
+    boolean doUrticaceae = include && exists;
 
 
-
-//    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
+    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
 //	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
 //	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();
-	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();
+//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();
 
 
 	//feature tree uuid
diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java
index d4c73d4a..3bd6db9f 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/cuba/CubaExcelImport.java
@@ -675,13 +675,13 @@ public class CubaExcelImport extends ExcelImporterBase<CubaImportState> {
     protected void firstPass(CubaImportState state) {
 	    boolean isSynonym = false;
 
-        int line = state.getCurrentLine();
+        String line = state.getCurrentLine() + ": ";
         HashMap<String, String> record = state.getOriginalRecord();
 
         Set<String> keys = record.keySet();
         for (String key: keys) {
             if (! expectedKeys.contains(key)){
-                logger.warn("Unexpected Key: " + key);
+                logger.warn(line + "Unexpected Key: " + key);
             }
         }
 
@@ -694,10 +694,10 @@ public class CubaExcelImport extends ExcelImporterBase<CubaImportState> {
         TaxonNode familyTaxon = getFamilyTaxon(record, state);
         if (familyTaxon == null){
             if (record.get("Taxón") != null){
-                logger.warn(line + ": Family not recognized but taxon exists: " + record.get("Taxón"));
+                logger.warn(line + "Family not recognized but taxon exists: " + record.get("Taxón"));
                 return;
             }else if (record.get("Syn.") == null){
-                logger.warn(line + ": Family not recognized but also no synonym exists");
+                logger.warn(line + "Family not recognized but also no synonym exists");
                 return;
             }else{
                 isSynonym = true;
@@ -710,7 +710,7 @@ public class CubaExcelImport extends ExcelImporterBase<CubaImportState> {
         //Taxón
         Taxon taxon = makeTaxon(record, state, familyTaxon, isSynonym);
         if (taxon == null && ! isSynonym){
-            logger.warn(line + ": taxon could not be created and is null");
+            logger.warn(line + "taxon could not be created and is null");
             return;
         }
         state.setCurrentTaxon(taxon);
-- 
2.34.1