diff --git a/src/main/java/org/jbei/ice/lib/entry/sequence/SequenceUtil.java b/src/main/java/org/jbei/ice/lib/entry/sequence/SequenceUtil.java index 5e9d6b39c..c3ecd0f28 100644 --- a/src/main/java/org/jbei/ice/lib/entry/sequence/SequenceUtil.java +++ b/src/main/java/org/jbei/ice/lib/entry/sequence/SequenceUtil.java @@ -136,7 +136,8 @@ static FeaturedDNASequence sequenceToDNASequence(Sequence sequence, List 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()) { diff --git a/src/main/java/org/jbei/ice/lib/entry/sequence/composers/formatters/GenbankFormatter.java b/src/main/java/org/jbei/ice/lib/entry/sequence/composers/formatters/GenbankFormatter.java index b3e85a9f5..cbe14bc0f 100755 --- a/src/main/java/org/jbei/ice/lib/entry/sequence/composers/formatters/GenbankFormatter.java +++ b/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; } -} \ No newline at end of file +} diff --git a/src/main/java/org/jbei/ice/services/rest/PartResource.java b/src/main/java/org/jbei/ice/services/rest/PartResource.java index b5fe6fd20..afb2eba4d 100644 --- a/src/main/java/org/jbei/ice/services/rest/PartResource.java +++ b/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 diff --git a/src/main/webapp/index.htm b/src/main/webapp/index.htm index 92e426f73..6c8a67a9e 100644 --- a/src/main/webapp/index.htm +++ b/src/main/webapp/index.htm @@ -6,7 +6,7 @@ ICE - Inventory of Composable Elements - + @@ -97,7 +97,7 @@ - +
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