Merge branch '5.9.0'

Author: hplahar

src/main/java/org/jbei/ice/lib/entry/sequence/SequenceUtil.java

@@ -136,7 +136,8 @@ static FeaturedDNASequence sequenceToDNASequence(Sequence sequence, List<Sequenc
                 }
 
                 dnaFeature.setId(sequenceFeature.getId());
-                dnaFeature.setType(sequenceFeature.getGenbankType());
+                String type = sequenceFeature.getFeature() != null && !StringUtils.isEmpty(sequenceFeature.getFeature().getGenbankType()) ? sequenceFeature.getFeature().getGenbankType() : sequenceFeature.getGenbankType();
+                dnaFeature.setType(type);
                 String name = sequenceFeature.getFeature() != null ? sequenceFeature.getFeature().getName() : sequenceFeature.getName();
                 dnaFeature.setName(name);
                 dnaFeature.setStrand(sequenceFeature.getStrand());

src/main/java/org/jbei/ice/lib/entry/sequence/composers/formatters/GFF3Formatter.java

@@ -41,7 +41,8 @@ public void format(Sequence sequence, OutputStream outputStream) throws IOExcept
         Set<SequenceFeature> featureSet = sequence.getSequenceFeatures();
         if (featureSet != null) {
             for (SequenceFeature sequenceFeature : featureSet) {
-                String featureLine = sequenceFeature.getName() + " ICE " + sequenceFeature.getGenbankType();
+                String featureType = sequenceFeature.getFeature() != null && !StringUtils.isEmpty(sequenceFeature.getFeature().getGenbankType()) ? sequenceFeature.getFeature().getGenbankType() : sequenceFeature.getGenbankType();
+                String featureLine = sequenceFeature.getName() + " ICE " + featureType;
 
                 // location
                 for (AnnotationLocation location : sequenceFeature.getAnnotationLocations()) {

src/main/java/org/jbei/ice/lib/entry/sequence/composers/formatters/GenbankFormatter.java

@@ -1,5 +1,6 @@
 package org.jbei.ice.lib.entry.sequence.composers.formatters;
 
+import org.apache.commons.lang3.StringUtils;
 import org.biojava.bio.seq.DNATools;
 import org.biojava.bio.seq.Feature;
 import org.biojava.bio.symbol.Location;
@@ -229,15 +230,13 @@ protected RichAnnotation getAnnotations(SequenceFeature sequenceFeature) {
      * @return Genbank Feature type.
      */
     protected String getFeatureType(SequenceFeature sequenceFeature) {
-        String featureType;
+        String featureType = sequenceFeature.getFeature() != null && !StringUtils.isEmpty(sequenceFeature.getFeature().getGenbankType()) ? sequenceFeature.getFeature().getGenbankType() : sequenceFeature.getGenbankType();
 
-        if (sequenceFeature.getGenbankType() == null || sequenceFeature.getGenbankType().isEmpty()) {
+        if (StringUtils.isEmpty(featureType)) {
             Logger.warn("SequenceFeature by id: " + sequenceFeature.getId()
                     + " has invalid genbank type.");
 
             featureType = "misc_feature";
-        } else {
-            featureType = sequenceFeature.getGenbankType();
         }
 
         return featureType;
@@ -301,4 +300,4 @@ private String normalizeFeatureValue(String value) {
 
         return result;
     }
-}
+}

src/main/java/org/jbei/ice/services/rest/PartResource.java

@@ -60,10 +60,10 @@
 @Path("/parts")
 public class PartResource extends RestResource {
 
-    private EntryController controller = new EntryController();
-    private Attachments attachments = new Attachments();
-    private SampleService sampleService = new SampleService();
-    private RemoteEntries remoteEntries = new RemoteEntries();
+    private final EntryController controller = new EntryController();
+    private final Attachments attachments = new Attachments();
+    private final SampleService sampleService = new SampleService();
+    private final RemoteEntries remoteEntries = new RemoteEntries();
 
     /**
      * Retrieves a part using any of the unique identifiers. e.g. Part number, synthetic id, or

src/main/webapp/index.htm

@@ -6,7 +6,7 @@
     <meta charset="utf-8">
     <title>ICE - Inventory of Composable Elements</title>
 
-    <link rel="stylesheet" type="text/css" href="scripts/lib/open-vector-editor-10.2.4/main.css">
+    <link rel="stylesheet" type="text/css" href="scripts/lib/open-vector-editor/main.css">
     <link href="css/font-awesome.min.css" rel="stylesheet">
     <link rel="stylesheet" href="scripts/lib/handsontable-7.1.0/pikaday.css">
     <link rel="stylesheet" media="screen" href="scripts/lib/handsontable-7.1.0/handsontable.full.min.css">
@@ -97,7 +97,7 @@
 </head>
 
 <body>
-<script type="text/javascript" src="scripts/lib/open-vector-editor-10.2.4/open-vector-editor.min.js"></script>
+<script type="text/javascript" src="scripts/lib/open-vector-editor/open-vector-editor.min.js"></script>
 
 <div id="container">
     <div id="body" ui-view></div>