From 3f7e2d6c74c56e3fb35b8b8aca6521e5a8f27e92 Mon Sep 17 00:00:00 2001
From: Hector Plahar <haplahar@lbl.gov>
Date: Wed, 23 Dec 2020 09:00:37 -1000
Subject: [PATCH 1/3] bug fix: properly convert openVE notes model to ICE model

---
 src/main/webapp/scripts/entry/entryController.js | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/main/webapp/scripts/entry/entryController.js b/src/main/webapp/scripts/entry/entryController.js
index 6868b0b53..9e21a524b 100644
--- a/src/main/webapp/scripts/entry/entryController.js
+++ b/src/main/webapp/scripts/entry/entryController.js
@@ -647,12 +647,22 @@ angular.module('ice.entry.controller', [])
                                         type: feature.type,
                                         name: feature.name,
                                         strand: feature.forward ? 1 : -1,
-                                        notes: [{name: "note", value: feature.notes}],
                                         locations: [{
                                             genbankStart: feature.start + 1,
                                             end: feature.end + 1
                                         }]
                                     };
+
+                                    // set notes
+                                    if (feature.notes) {
+                                        featureMap[feature.id].notes = [];
+                                        for (const prop in feature.notes) {
+                                            if (!feature.notes.hasOwnProperty(prop))
+                                                continue;
+
+                                            featureMap[feature.id].notes.push({name: "note", value: prop})
+                                        }
+                                    }
                                 }
                             }
 
@@ -663,6 +673,8 @@ angular.module('ice.entry.controller', [])
                                 sequence.features.push(featureMap[property]);
                             }
 
+                            console.log(sequence.features);
+
                             Util.update("rest/parts/" + entry.id + "/sequence", sequence, {},
                                 function (result) {
                                     console.log("save completed for", entry.id);

From 3b78fa15612d0b6df706db4ef053e35c4c1da26f Mon Sep 17 00:00:00 2001
From: Hector Plahar <haplahar@lbl.gov>
Date: Tue, 5 Jan 2021 14:19:42 -0800
Subject: [PATCH 2/3] bug fix: update feature on name or type change

---
 .../jbei/ice/lib/entry/sequence/PartSequence.java    | 12 ++++++++++++
 .../jbei/ice/lib/entry/sequence/SequenceUtil.java    |  3 ++-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java b/src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java
index a42784af0..7a3f61ff4 100644
--- a/src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java
+++ b/src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java
@@ -362,6 +362,18 @@ private void checkForUpdatedFeatures(Sequence existing, Sequence updated) {
             // for each existing feature, check with updated for difference in name and type
             for (SequenceFeature updatedSequenceFeature : updated.getSequenceFeatures()) {
                 Feature sequenceFeature = updatedSequenceFeature.getFeature();
+                Feature existingFeatureFeature = existingFeature.getFeature();
+
+                if (!sequenceFeature.getHash().equals(existingFeatureFeature.getHash()))
+                    continue;
+
+                if (!sequenceFeature.getName().equals(existingFeatureFeature.getName()) ||
+                        !sequenceFeature.getGenbankType().equals(existingFeatureFeature.getGenbankType())) {
+                    // update
+                    existingFeatureFeature.setName(sequenceFeature.getName());
+                    existingFeatureFeature.setGenbankType(sequenceFeature.getGenbankType());
+                    featureDAO.update(existingFeatureFeature);
+                }
             }
         }
     }
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 67fd1e627..5e9d6b39c 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
@@ -137,7 +137,8 @@ static FeaturedDNASequence sequenceToDNASequence(Sequence sequence, List<Sequenc
 
                 dnaFeature.setId(sequenceFeature.getId());
                 dnaFeature.setType(sequenceFeature.getGenbankType());
-                dnaFeature.setName(sequenceFeature.getName());
+                String name = sequenceFeature.getFeature() != null ? sequenceFeature.getFeature().getName() : sequenceFeature.getName();
+                dnaFeature.setName(name);
                 dnaFeature.setStrand(sequenceFeature.getStrand());
 
                 if (sequenceFeature.getAnnotationType() != null) {

From 0b275b51f0a1647975eff5b4e438173d460a752b Mon Sep 17 00:00:00 2001
From: Hector Plahar <haplahar@lbl.gov>
Date: Thu, 7 Jan 2021 08:20:55 -0800
Subject: [PATCH 3/3] version 5.8.2 label

---
 pom.xml                                                 | 2 +-
 src/main/java/org/jbei/ice/lib/config/SiteSettings.java | 2 +-
 src/main/webapp/views/footer.html                       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index c3643e137..490a4e048 100755
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>5.8.1</version>
+    <version>5.8.2</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>
diff --git a/src/main/java/org/jbei/ice/lib/config/SiteSettings.java b/src/main/java/org/jbei/ice/lib/config/SiteSettings.java
index 690c0df92..ef6fefd57 100644
--- a/src/main/java/org/jbei/ice/lib/config/SiteSettings.java
+++ b/src/main/java/org/jbei/ice/lib/config/SiteSettings.java
@@ -9,7 +9,7 @@
  */
 public class SiteSettings implements IDataTransferModel {
 
-    private String version = "5.8.1";
+    private String version = "5.8.2";
     private String assetName;
     private boolean hasLogo;
     private boolean hasLoginMessage;
diff --git a/src/main/webapp/views/footer.html b/src/main/webapp/views/footer.html
index abe97647f..04c8db1ac 100644
--- a/src/main/webapp/views/footer.html
+++ b/src/main/webapp/views/footer.html
@@ -11,7 +11,7 @@
     </div>
     <div class="text-right" style="white-space: nowrap;">
         &copy;&nbsp;<a href="https://github.com/JBEI/ice">JBEI ICE Registry</a> <span
-            class="label label-primary">5.8.1</span><br>
+            class="label label-primary">5.8.2</span><br>
         All rights reserved. <br>
         <a href="https://github.com/JBEI/ice/issues/new">Submit an Issue</a>&nbsp; <span class="text-muted">|</span>
         &nbsp;<a href="http://ice.jbei.org/">Help</a>