From e6a3d605c44a4e07f7d9d846df536035f623295e Mon Sep 17 00:00:00 2001
From: =?utf8?q?Andreas=20M=C3=BCller?= <a.mueller@bgbm.org>
Date: Thu, 15 Mar 2012 14:50:16 +0000
Subject: [PATCH] bugfixes for IF

---
 ...dexFungorumHigherClassificationImport.java | 20 ++++++-----
 .../IndexFungorumImportBase.java              | 36 ++++++++++++-------
 2 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java
index 7cdf8358..a82650ac 100644
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java
@@ -16,7 +16,6 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.UUID;
 
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Component;
@@ -24,7 +23,7 @@ import org.springframework.transaction.TransactionStatus;
 
 import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
 import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.location.NamedArea;
+import eu.etaxonomy.cdm.model.common.Marker;
 import eu.etaxonomy.cdm.model.name.BotanicalName;
 import eu.etaxonomy.cdm.model.name.NonViralName;
 import eu.etaxonomy.cdm.model.name.Rank;
@@ -133,8 +132,8 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
 											higherTaxon = taxonKingdom;
 										}
 										higherTaxon = isIncertisSedis(kingdom) ? higherTaxon : taxonKingdom;
-										Rank rank = (lastKingdom.equals("Fungi") ? Rank.DIVISION() : Rank.PHYLUM());
-										taxonPhylum = makeTaxon(state, phylum, rank);
+										Rank newRank = (lastKingdom.equals("Fungi") ? null : Rank.PHYLUM());
+										taxonPhylum = makeTaxon(state, phylum, newRank);
 										if (taxonPhylum != null){
 											classification.addParentChild(higherTaxon, taxonPhylum, null, null);
 										}
@@ -144,8 +143,8 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
 									}else{
 										higherTaxon = taxonPhylum;
 									}
-									Rank rank = (lastKingdom.equals("Fungi") ? Rank.SUBDIVISION() : Rank.SUBPHYLUM());
-									taxonSubphylum = makeTaxon(state, subphylum, rank);
+									Rank newRank = (lastKingdom.equals("Fungi") ? null : Rank.SUBPHYLUM());
+									taxonSubphylum = makeTaxon(state, subphylum, newRank);
 									if (taxonSubphylum != null){
 										getClassification(state).addParentChild(higherTaxon,taxonSubphylum, null, null);
 									}
@@ -237,19 +236,22 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
 		return result;
 	}
 
-	private Taxon makeTaxon(IndexFungorumImportState state, String uninomial, Rank rank) {
+	private Taxon makeTaxon(IndexFungorumImportState state, String uninomial, Rank newRank) {
 		if (uninomial.equalsIgnoreCase(INCERTAE_SEDIS) || uninomial.equalsIgnoreCase(FOSSIL_FUNGI)){
 			return null;
 		}
 		Taxon taxon = state.getRelatedObject(IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES, uninomial, Taxon.class);
 		if (taxon == null){
-			if (! rank.equals(Rank.KINGDOM())){
+			if (! newRank.equals(Rank.KINGDOM())){
 				logger.warn("Taxon not found for " + uninomial);
 			}
-			NonViralName<?> name = BotanicalName.NewInstance(rank);
+			NonViralName<?> name = BotanicalName.NewInstance(newRank);
 			name.setGenusOrUninomial(uninomial);
 			Reference<?> sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
 			taxon = Taxon.NewInstance(name, sourceReference);
+			taxon.addMarker(Marker.NewInstance(getMissingGUIDMarkerType(state), true));
+		}else if (newRank != null){
+			taxon.getName().setRank(newRank);
 		}
 		return taxon;
 	}
diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportBase.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportBase.java
index c253d9e7..09a8c43f 100644
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportBase.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportBase.java
@@ -308,7 +308,7 @@ public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungoru
 		String location = rs.getString("pubIMIAbbrLoc");
 		if (StringUtils.isNotBlank(location)){
 			if (hasInReference){
-				ref.getInReference().setTitle(location);
+				ref.getInReference().setPlacePublished(location);
 			}else{
 				ref.setPlacePublished(location);
 			}
@@ -316,7 +316,12 @@ public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungoru
 		//title
 		String titleMain = rs.getString("pubIMIAbbr");
 		String supTitle = rs.getString("pubIMISupAbbr");
-		String title = CdmUtils.concat(" ", titleMain, supTitle);
+		String title = CdmUtils.concat(", ", titleMain, supTitle);
+		//preliminary to comply with current Index Fungorum display
+		if (StringUtils.isNotBlank(location)){
+			title += "(" + location +")";
+		}
+		//end preliminary
 		if (StringUtils.isNotBlank(title)){
 			if (hasInReference){
 				ref.getInReference().setTitle(title);
@@ -337,15 +342,15 @@ public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungoru
 		}
 		//year
 		String yearOfPubl = rs.getString("YEAR_OF_PUBLICATION");
-		String year = null;
 		String yearOnPubl = rs.getString("YEAR_ON_PUBLICATION");
+		String year = null;
 		if (StringUtils.isNotBlank(yearOfPubl)){
 			year = yearOfPubl.trim();
 		}
 		if (StringUtils.isNotBlank(yearOnPubl)){
 			year = CdmUtils.concat(" ", year, "[" + yearOnPubl + "]");
 		}
-		if (year == null){
+		if (year != null){
 			ref.setDatePublished(TimePeriod.parseString(year));
 		}
 		
@@ -353,11 +358,17 @@ public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungoru
 	}
 	
 
+	protected MarkerType getNoLastActionMarkerType(IndexFungorumImportState state) {
+		return getMarkerType(state, DbLastActionMapper.uuidMarkerTypeHasNoLastAction, 
+				"has no last action", "No last action information available", "no last action");
+	}
+
+
 	protected void makeSource(IndexFungorumImportState state, Taxon taxon, Integer id, String namespace) {
 		//source reference
 		Reference<?> sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
 		//source
-		String strId = String.valueOf(id);
+		String strId = (id == null ? null : String.valueOf(id));
 		IdentifiableSource source = IdentifiableSource.NewInstance(strId, namespace, sourceReference, null);
 		taxon.addSource(source);
 		
@@ -368,26 +379,25 @@ public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungoru
 		makeLSID(taxon, strId, state);
 	}
 
-	public MarkerType getNoLastActionMarkerType(IndexFungorumImportState state) {
-		MarkerType hasNoLastAction = getMarkerType(state, DbLastActionMapper.uuidMarkerTypeHasNoLastAction, 
-				"has no last action", "No last action information available", "no last action");
-		return hasNoLastAction;
-	}
-
 	private void makeLSID(Taxon taxon, String strId, IndexFungorumImportState state) {
 		try {
-			if (StringUtils.isNotBlank(strId) && ! "null".equalsIgnoreCase(strId)){
+			if (StringUtils.isNotBlank(strId) &&  strId != null){
 				LSID lsid = new LSID(IndexFungorumTransformer.LSID_PREFIX + strId);
 				taxon.setLsid(lsid);
 			}else{
 				logger.warn("No ID available for taxon " + taxon.getTitleCache() + ", " +  taxon.getUuid());
-				MarkerType missingGUID = getMarkerType(state, PesiTransformer.uuidMarkerGuidIsMissing, "GUID is missing", "GUID is missing", null);
+				MarkerType missingGUID = getMissingGUIDMarkerType(state);
 				taxon.addMarker(Marker.NewInstance(missingGUID, true));
 			}
 		} catch (MalformedLSIDException e) {
 			logger.error(e.getMessage());
 		}
 	}
+
+	protected MarkerType getMissingGUIDMarkerType(IndexFungorumImportState state) {
+		MarkerType missingGUID = getMarkerType(state, PesiTransformer.uuidMarkerGuidIsMissing, "GUID is missing", "GUID is missing", null);
+		return missingGUID;
+	}
 	
 
 	protected Classification getClassification(IndexFungorumImportState state) {
-- 
2.34.1