Update dependencies & bump version to track biojava

- biojava 6.0.0-alpha1 (fixes many bugs around RCSB legacy services)
- NGL 0.9.3
- MSAViewer 1.0

Author: sbliven

README.md

@@ -18,7 +18,7 @@ Deployment
 
 ```
 mvn package
-java -jar target/biojava-http-full-5.0.0-SNAPSHOT.jar
+java -jar target/biojava-http-full-6.0.0-SNAPSHOT.jar
 ```
 
 Access the following URLs:
@@ -27,3 +27,9 @@ Access the following URLs:
 http://localhost:8080/ngl/4hhb
 http://localhost:8080/cesymm/1hiv.A
 ```
+
+Libraries
+---------
+
+- [NGL](https://github.com/nglviewer/ngl)
+- [MSAViewer](http://msa.biojs.net/)

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava-http</artifactId>
-	<version>5.0.0-SNAPSHOT</version>
+	<version>6.0.0-SNAPSHOT</version>
 	<name>BioJava HTTP</name>
 	<description>HTML/JS based interfaces for BioJava</description>
 
@@ -15,7 +15,7 @@
 		<timestamp>${maven.build.timestamp}</timestamp>
 		<slf4j.version>1.7.19</slf4j.version>
 		<log4j.version>2.13.3</log4j.version>
-		<biojava.version>${project.version}</biojava.version>
+		<biojava.version>6.0.0-alpha1</biojava.version>
 	</properties>
 
 	<repositories>
@@ -30,7 +30,7 @@
 			</snapshots>
 		</repository>
 	</repositories>
-	
+
 	<scm>
 		<connection>scm:git:[email protected]:biojava/biojava-http.git</connection>
 		<developerConnection>scm:git:[email protected]:biojava/biojava-http.git</developerConnection>
@@ -120,7 +120,7 @@
 					<maxmem>2000m</maxmem>
 				</configuration>
 			</plugin>
-			
+
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-shade-plugin</artifactId>
@@ -173,7 +173,7 @@
 					</execution>
 				</executions>
 			</plugin>
-			
+
 			<!-- Include git commit -->
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>

src/main/java/org/biojava/http/models/NGLParams.java

@@ -18,24 +18,23 @@
  *      http://www.biojava.org/
  *
  * Created on Jul 6, 2016
- * Author: blivens 
+ * Author: blivens
  *
  */
- 
+
 package org.biojava.http.models;
- 
+
 public class NGLParams {
 	private String url;
 	private String structUrl;
 	private int size;
-	
+
 	public NGLParams(String structUrl) {
-		url = "https://cdn.rawgit.com/arose/ngl/v0.7.1a/js/build/ngl.embedded.min.js";
-		url = "https://rawgit.com/arose/ngl/master/dist/ngl.js";
+		url = "//cdn.jsdelivr.net/gh/nglviewer/[email protected]/dist/ngl.js";
 		this.structUrl = structUrl;
 		this.setSize(500);
 	}
-	
+
 	public String getUrl() {
 		return url;
 	}

src/main/resources/templates/cesymm.html.hbs

@@ -36,10 +36,10 @@ document.addEventListener( "DOMContentLoaded", function() {
 		if( lines.length > 0) {
 			// Get number of structures from first line
 			var n_strucs = (lines[0].length - 1) / 3;
-	
+
 			// Generate color palette
 			var colors = palette('cb-Dark2', n_strucs);
-	
+
 			// Create selection for each repeat
 			for (j = 0; j < n_strucs; j++) {
 				var seleStr = [];
@@ -55,6 +55,7 @@ document.addEventListener( "DOMContentLoaded", function() {
 		}
 		colorSele.push(["lightgrey","*"]);
 
+		// Note future NGL versions may rename to NGL.ColormakerRegistry
 		var schemeId = NGL.ColorMakerRegistry.addSelectionScheme( colorSele, "CE-Symm {{structureId}}" );
 
 		stage = new NGL.Stage( "viewport" );
@@ -72,9 +73,9 @@ document.addEventListener( "DOMContentLoaded", function() {
 } );
 
 </script>
-<script src="https://cdn.bio.sh/msa/latest/msa.min.gz.js"></script>
+<script src="//s3.eu-central-1.amazonaws.com/cdn.bio.sh/msa/1.0/msa.min.gz.js"></script>
 
-<script src="https://cdn.rawgit.com/google/palette.js/master/palette.js"></script>
+<script src="//cdn.jsdelivr.net/gh/google/palette.js@master/palette.js"></script>
 <!--script src="{{pallete_url}}"></script-->
 <script>
 var opts = {

src/main/resources/templates/cesymm_multi.html.hbs

@@ -36,10 +36,10 @@ document.addEventListener( "DOMContentLoaded", function() {
 		if( lines.length > 0) {
 			// Get number of structures from first line
 			var n_strucs = (lines[0].length - 1) / 3;
-	
+
 			// Generate color palette
 			var colors = palette('cb-Dark2', n_strucs);
-	
+
 			// Create selection for each repeat
 			var seleStr = [];
 			for (j = 0; j < n_strucs; j++) {
@@ -57,6 +57,7 @@ document.addEventListener( "DOMContentLoaded", function() {
 		}
 		colorSele.push(["lightgrey","*"]);
 
+		// Note future NGL versions may rename to NGL.ColormakerRegistry
 		var schemeId = NGL.ColorMakerRegistry.addSelectionScheme( colorSele, "CE-Symm {{structureId}}" );
 
 		stage = new NGL.Stage( "viewport" );
@@ -76,7 +77,7 @@ document.addEventListener( "DOMContentLoaded", function() {
 </script>
 
 
-<script src="https://cdn.bio.sh/msa/latest/msa.min.gz.js"></script>
+<script src="https://s3.eu-central-1.amazonaws.com/cdn.bio.sh/msa/latest/msa.min.gz.js"></script>
 
 <script src="https://cdn.rawgit.com/google/palette.js/master/palette.js"></script>
 <!--script src="{{pallete_url}}"></script-->