cleanup

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / specimen / abcd206 / in / AbcdParseUtility.java

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/AbcdParseUtility.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/AbcdParseUtility.java
index 4742d9411ef45bbf027d1adc547c33a856a4fd54..60af747c15290ea79d09059cbeb6725732d53aa4 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/AbcdParseUtility.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/AbcdParseUtility.java
@@ -1,4 +1,3 @@
-// $Id$
 /**
 * Copyright (C) 2015 EDIT
 * European Distributed Institute of Taxonomy
@@ -9,32 +8,45 @@
 */
 package eu.etaxonomy.cdm.io.specimen.abcd206.in;
 
+import java.io.InputStream;
 import java.net.URI;
 import java.util.Date;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
 
 import org.apache.log4j.Logger;
 import org.joda.time.DateTime;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
+import eu.etaxonomy.cdm.api.application.ICdmRepository;
+import eu.etaxonomy.cdm.common.CdmUtils;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
+import eu.etaxonomy.cdm.persistence.query.MatchMode;
+
 /**
  * @author pplitzner
- * @date 16.06.2015
- *
+ * @since 16.06.2015
  */
 public class AbcdParseUtility {
 
     private static final Logger logger = Logger.getLogger(AbcdParseUtility.class);
 
-
-    public static URI parseFirstUri(NodeList nodeList){
+    public static URI parseFirstUri(NodeList nodeList, SpecimenImportReport report){
         URI uri = null;
         String textContent = parseFirstTextContent(nodeList);
         if(textContent!=null){
             try {
                 uri = URI.create(textContent);
             } catch (IllegalArgumentException e) {
-                //nothing
+                if(report!=null){
+                    report.addException("Exception during URI parsing!", e);
+                }
             }
         }
         return uri;
@@ -46,7 +58,7 @@ public class AbcdParseUtility {
 
     public static String parseFirstTextContent(NodeList nodeList, boolean cleanUpWhiteSpaces){
         String string = null;
-        if(nodeList.getLength()>0){
+        if(nodeList!=null && nodeList.getLength()>0){
             string = nodeList.item(0).getTextContent();
             if(cleanUpWhiteSpaces){
                 string = string.replace("\n", "").replaceAll("( )+", " ").trim();
@@ -55,14 +67,14 @@ public class AbcdParseUtility {
         return string;
     }
 
-    public static Double parseFirstDouble(NodeList nodeList){
+    public static Double parseFirstDouble(NodeList nodeList, SpecimenImportReport report){
         if(nodeList.getLength()>0){
-            return parseDouble(nodeList.item(0));
+            return parseDouble(nodeList.item(0), report);
         }
         return null;
     }
 
-    public static Double parseDouble(Node node){
+    public static Double parseDouble(Node node, SpecimenImportReport report){
         String message = "Could not parse double value for node " + node.getNodeName();
         Double doubleValue = null;
         try{
@@ -71,11 +83,19 @@ public class AbcdParseUtility {
             textContent = textContent.replace(".","");
             //convert commmas
             textContent = textContent.replace(",",".");
-            doubleValue = Double.parseDouble(textContent);
+            if (!CdmUtils.isBlank(textContent)){
+                doubleValue = Double.parseDouble(textContent);
+            }
         } catch (NullPointerException npe){
             logger.error(message, npe);
+            if(report!=null){
+                report.addException(message, npe);
+            }
         } catch (NumberFormatException nfe){
             logger.error(message, nfe);
+            if(report!=null){
+                report.addException(message, nfe);
+            }
         }
         return doubleValue;
     }
@@ -92,8 +112,65 @@ public class AbcdParseUtility {
     public static Date parseFirstDate(NodeList nodeList) {
         Date date = null;
         DateTime dateTime = parseFirstDateTime(nodeList);
-        date = dateTime.toDate();
+        if(dateTime!=null){
+            date = dateTime.toDate();
+        }
         return date;
     }
 
-}
+    public static Reference parseFirstReference(NodeList referenceNodeList, ICdmRepository cdmAppController){
+        String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceNodeList);
+        //check if reference already exists
+        List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitleWithRestrictions(Reference.class, referenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();
+        Reference reference;
+        if(matchingReferences.size()==1){
+            reference = matchingReferences.iterator().next();
+        }
+        else{
+            reference = ReferenceFactory.newGeneric();
+            reference.setTitle(referenceCitation);
+            cdmAppController.getReferenceService().saveOrUpdate(reference);
+        }
+        return reference;
+    }
+
+    /**
+     * Return the wrapper with the list of root nodes for an ABCD XML file
+     * @param fileName: the file's location
+     * @return a wrapper with a list of root nodes ("Unit")
+     */
+    public static UnitAssociationWrapper parseUnitsNodeList(InputStream inputStream, SpecimenImportReport report) {
+        UnitAssociationWrapper unitAssociationWrapper = new UnitAssociationWrapper();
+        NodeList unitList = null;
+        try {
+            DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+            DocumentBuilder builder = factory.newDocumentBuilder();
+
+            Document document = builder.parse(inputStream);
+            Element root = document.getDocumentElement();
+            unitList = root.getElementsByTagName("Unit");
+            if (unitList.getLength()>0) {
+                unitAssociationWrapper.setPrefix("");
+                unitAssociationWrapper.setAssociatedUnits(unitList);
+                return unitAssociationWrapper;
+            }
+            unitList = root.getElementsByTagName("abcd:Unit");
+            if (unitList.getLength()>0) {
+                unitAssociationWrapper.setPrefix("abcd:");
+                unitAssociationWrapper.setAssociatedUnits(unitList);
+                return unitAssociationWrapper;
+            }
+            unitList = root.getElementsByTagName("abcd21:Unit");
+            if (unitList.getLength()>0) {
+                unitAssociationWrapper.setPrefix("abcd21:");
+                unitAssociationWrapper.setAssociatedUnits(unitList);
+            }
+        } catch (Exception e) {
+            logger.warn(e);
+            if(report!=null){
+                report.addException("Exception during parsing of nodeList!", e);
+            }
+        }
+        return unitAssociationWrapper;
+    }
+}
\ No newline at end of file