Merge branch '5.9.1'

JBEI · May 10, 2021 · 8add227 · 8add227
2 parents c1b870e + 97c3734
commit 8add227
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Showing 9 changed files with 68 additions and 141 deletions.
diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ To install in a production environment, please [consult our manual](http://ice.j
 ### Development
 To set up a development environment or local machine installation make sure you have the following dependencies installed
 
-* [Java JDK 8](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
+* [Open JDK 15](https://openjdk.java.net/projects/jdk/15/)
 * [Maven 3](https://maven.apache.org/download.cgi)
 * [Git](https://git-scm.com/downloads)
 
@@ -49,8 +49,5 @@ Command line installation steps (linux environment):
 ## Links
 * [Documentation](http://ice.jbei.org/) including user manual and API documentation
 
-## Build Status:
-[![Build Status](https://travis-ci.org/JBEI/ice.svg?branch=master)](https://travis-ci.org/JBEI/ice)
-
 ## Related Projects
 [Open Vector Editor](https://github.com/TeselaGen/openVectorEditor) is used in ICE to display and edit sequences
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>5.9.0</version>
+    <version>5.9.1</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>
@@ -91,7 +91,7 @@
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>2.6</version>
+            <version>2.8.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -131,6 +131,11 @@
             <artifactId>jta</artifactId>
             <version>1.1</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-compiler-plugin</artifactId>
+            <version>3.8.1</version>
+        </dependency>
         <dependency>
             <groupId>org.sbolstandard</groupId>
             <artifactId>libSBOLj</artifactId>
@@ -183,35 +188,10 @@
                 </excludes>
             </testResource>
         </testResources>
-        <plugins>
-            <plugin>
-                <inherited>true</inherited>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.8.1</version>
-                <configuration>
-                    <source>13</source>
-                    <target>13</target>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.1.1</version>
-                <configuration>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-war-plugin</artifactId>
-                <version>3.2.3</version>
-                <configuration>
-                    <attachClasses>true</attachClasses>
-                </configuration>
-            </plugin>
-        </plugins>
     </build>
     <properties>
+        <maven.compiler.source>15</maven.compiler.source>
+        <maven.compiler.target>15</maven.compiler.target>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     </properties>

diff --git 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 = "5.9.0";
+    private String version = "5.9.1";
     private String assetName;
     private boolean hasLogo;
     private boolean hasLoginMessage;

diff --git a/src/main/webapp/scripts/entry/entryController.js b/src/main/webapp/scripts/entry/entryController.js
@@ -711,7 +711,7 @@ angular.module('ice.entry.controller', [])
 
                         onCopy: function (event, copiedSequenceData, editorState) {
                             let clipboardData = event.clipboardData || window.clipboardData || event.originalEvent.clipboardData;
-                            clipboardData.setData('text/plain', copiedSequenceData.sequence);
+                            // clipboardData.setData('text/plain', copiedSequenceData.sequence);
                             openVEData.selection = editorState.selectionLayer;
                             openVEData.openVECopied = copiedSequenceData;
                             clipboardData.setData('application/json', JSON.stringify(openVEData));

diff --git a/src/main/webapp/scripts/entry/entryDirectives.js b/src/main/webapp/scripts/entry/entryDirectives.js
@@ -103,7 +103,7 @@ angular.module('ice.entry.directives', [])
                     $scope.editor = $window.createVectorEditor(document.getElementById("ve-Root"), {
                         onCopy: function (event, sequenceData, editorState) {
                             const clipboardData = event.clipboardData || window.clipboardData || event.originalEvent.clipboardData;
-                            clipboardData.setData('text/plain', sequenceData.sequence);
+                            // clipboardData.setData('text/plain', sequenceData.sequence);
                             data.selection = editorState.selectionLayer;
                             data.openVECopied = sequenceData;
                             clipboardData.setData('application/json', JSON.stringify(data));

diff --git a/src/main/webapp/scripts/entry/traces/tracesController.js b/src/main/webapp/scripts/entry/traces/tracesController.js
@@ -137,8 +137,12 @@ angular.module('ice.entry.traces.controller', [])
 //            }
 
 
-                var alignment = {
+                const alignment = {
                     id: "iceAlignment",
+                    alignmentName: 'Untitled', // todo
+                    alignmentAnnotationVisibility: {
+                        "features": true,
+                    },
                     pairwiseAlignments: []
                 };
 

diff --git a/src/main/webapp/scripts/lib/open-vector-editor/main.css b/src/main/webapp/scripts/lib/open-vector-editor/main.css
diff --git a/src/main/webapp/scripts/lib/open-vector-editor/open-vector-editor.min.js b/src/main/webapp/scripts/lib/open-vector-editor/open-vector-editor.min.js
diff --git 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">5.9.0</span><br>
+            class="label label-primary">5.9.1</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>