Import missing parameters for ggbn ABCD import

 - some refactoring

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java
index 7ac9187c7430603b7e627e4da9385a9608dd55b1..92f710b35763c8b77e35a4f7f76dbd3acfd33733 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java
@@ -93,6 +93,9 @@ import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
  */
 @Component
 public class Abcd206Import extends SpecimenImportBase<Abcd206ImportConfigurator, Abcd206ImportState> {
+
+    private static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
+
     private static final Logger logger = Logger.getLogger(Abcd206Import.class);
 
     private final boolean DEBUG = true;
@@ -377,7 +380,7 @@ public class Abcd206Import extends SpecimenImportBase<Abcd206ImportConfigurator,
                             //add media also as specimen scan
                             MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.Media);
                             mediaSpecimen.setMediaSpecimen(media);
-                            DefinedTermBase specimenScanTerm = getTermService().load(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"));
+                            DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);
                             if(specimenScanTerm instanceof DefinedTerm){
                                 mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
                             }

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 0516a9232f3c8065d475c3a52a9dc771785accb3..b62c06bf044e352a3be623e1eae1877721b3523b 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
@@ -12,6 +12,7 @@ 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;
@@ -23,6 +24,11 @@ import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
+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
@@ -112,6 +118,22 @@ public class AbcdParseUtility {
         return date;
     }
 
+    public static Reference parseFirstReference(NodeList referenceNodeList, ICdmApplicationConfiguration cdmAppController){
+        String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceNodeList);
+        //check if reference already exists
+        List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitle(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

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/molecular/AbcdGgbnParser.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/molecular/AbcdGgbnParser.java
index cf337a9229e76e19099a38456e291673d0cefc12..4d77b08c87b8ee8d56f17e1c7fe524ed30b632df 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/molecular/AbcdGgbnParser.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/molecular/AbcdGgbnParser.java
@@ -11,6 +11,7 @@ package eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular;
 
 import java.net.URI;
 import java.util.List;
+import java.util.UUID;
 
 import org.apache.log4j.Logger;
 import org.w3c.dom.Element;
@@ -23,6 +24,7 @@ import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
 import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
 import eu.etaxonomy.cdm.model.common.DefinedTerm;
 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
+import eu.etaxonomy.cdm.model.common.OrderedTerm;
 import eu.etaxonomy.cdm.model.media.Media;
 import eu.etaxonomy.cdm.model.molecular.Amplification;
 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
@@ -35,7 +37,6 @@ import eu.etaxonomy.cdm.model.molecular.SequenceString;
 import eu.etaxonomy.cdm.model.molecular.SingleRead;
 import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
 import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
 import eu.etaxonomy.cdm.persistence.query.MatchMode;
 
 /**
@@ -45,6 +46,14 @@ import eu.etaxonomy.cdm.persistence.query.MatchMode;
  */
 public class AbcdGgbnParser {
 
+    //DNA Quality term
+    private static final String HIGH = "high";
+    private static final String MEDIUM = "medium";
+    private static final String LOW = "low";
+    private static final UUID HIGH_QUALITY_TERM = UUID.fromString("ec443c76-5987-4ec5-a66b-da207f70b47f");
+    private static final UUID MEDIUM_QUALITY_TERM = UUID.fromString("2a174892-1246-4807-9022-71ce8639346b");
+    private static final UUID LOW_QUALITY_TERM = UUID.fromString("a3bf12ff-b041-425f-bdaa-aa51da65eebc");
+
     private static final String FORWARD = "forward";
 
     private static final String REVERSE = "reverse";
@@ -92,8 +101,8 @@ public class AbcdGgbnParser {
         DnaQuality dnaQuality = DnaQuality.NewInstance();
 
         NodeList purificationMethodList = element.getElementsByTagName(prefix+"purificationMethod");
-        //TODO
-//        dnaQuality.setPurificationMethod(purificationMethod)
+        String purificationMethod = AbcdParseUtility.parseFirstTextContent(purificationMethodList);
+        dnaQuality.setPurificationMethod(purificationMethod);
 
         NodeList concentrationList = element.getElementsByTagName(prefix+"concentration");
         if(concentrationList.getLength()==1){
@@ -118,10 +127,19 @@ public class AbcdGgbnParser {
         }
 
         NodeList qualityList = element.getElementsByTagName(prefix+"quality");
+        String quality = AbcdParseUtility.parseFirstTextContent(qualityList);
+        if(LOW.equals(quality)){
+            dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(LOW_QUALITY_TERM));
+        }
+        else if(MEDIUM.equals(quality)){
+            dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(MEDIUM_QUALITY_TERM));
+        }
+        else if(HIGH.equals(quality)){
+            dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(HIGH_QUALITY_TERM));
+        }
+
         NodeList qualityRemarksList = element.getElementsByTagName(prefix+"qualityRemarks");
 
-        //TODO
-//        dnaQuality.setQualityTerm(qualityTerm)
 
         return dnaQuality;
     }
@@ -187,7 +205,7 @@ public class AbcdGgbnParser {
                     parseAmplificationPrimers(amplificationElement.getElementsByTagName(prefix+"AmplificationPrimers"));
                 }
             }
-            //check if amplification already exists
+            //check if amplification already exists (can only be checked after all fields are initialized because comparison is done on the label cache))
             List<Amplification> matchingAmplifications = cdmAppController.getAmplificationService().findByLabelCache(amplification.getLabelCache(), MatchMode.EXACT, null, null, null, null, null).getRecords();
             if(matchingAmplifications.size()==1){
                 amplification = matchingAmplifications.iterator().next();
@@ -253,21 +271,10 @@ public class AbcdGgbnParser {
             if(referenceList.item(i) instanceof Element){
                 Element element = (Element)referenceList.item(i);
                 NodeList referenceCitationList = element.getElementsByTagName(prefix+"ReferenceCitation");
-                String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceCitationList);
-                List<Reference> matchedReferences = cdmAppController.getReferenceService().findByTitle(Reference.class, referenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();
-                Reference<?> reference;
-                if(matchedReferences.size()==1){
-                    reference = matchedReferences.iterator().next();
-                }
-                else{
-                    reference = ReferenceFactory.newGeneric();
-                    reference.setTitle(referenceCitation);
-                    cdmAppController.getReferenceService().saveOrUpdate(reference);
-                }
+                Reference reference = AbcdParseUtility.parseFirstReference(referenceCitationList, cdmAppController);
                 sequence.addCitation(reference);
             }
         }
-
     }
 
     private void parseSingleSequencings(NodeList singleSequencingsList, Amplification amplification, AmplificationResult amplificationResult, Sequence sequence) {
@@ -337,17 +344,8 @@ public class AbcdGgbnParser {
                     //reference citation
                     NodeList primerReferenceCitationList = sequencingPrimer.getElementsByTagName(prefix+"primerReferenceCitation");
                     String primerReferenceCitation = AbcdParseUtility.parseFirstTextContent(primerReferenceCitationList);
-                    List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitle(Reference.class, primerReferenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();
-                    Reference<?> primerReference;
-                    if(matchingReferences.size()==1){
-                        primerReference = matchingReferences.iterator().next();
-                    }
-                    else{
-                        primerReference = ReferenceFactory.newGeneric();
-                        primerReference.setTitle(primerReferenceCitation);
-                        cdmAppController.getReferenceService().saveOrUpdate(primerReference);
-                    }
-                    primer.setPublishedIn(primerReference);
+                    Reference reference = AbcdParseUtility.parseFirstReference(primerReferenceCitationList, cdmAppController);
+                    primer.setPublishedIn(reference);
 
                     cdmAppController.getPrimerService().save(primer);
                 }