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sblivensbliven
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Add cesymm route
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8 files changed

+184
-13
lines changed

8 files changed

+184
-13
lines changed

‎pom.xml‎

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@@ -89,6 +89,12 @@
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<artifactId>spark-template-handlebars</artifactId>
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<version>2.3</version>
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</dependency>
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<dependency>
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<groupId>com.google.code.gson</groupId>
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<artifactId>gson</artifactId>
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<version>2.7</version>
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</dependency>
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</dependencies>
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<build>

‎src/main/java/org/biojava/http/BioJavaRoutes.java‎

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@@ -28,4 +28,5 @@ public class BioJavaRoutes {
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public static String PDB = "/pdb/:id";
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public static String MMCIF = "/mmcif/:id";
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public static String NGL = "/ngl/:id";
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public static String CESYMM_JSON = "/cesymm/:id/json";
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}

‎src/main/java/org/biojava/http/ServerMain.java‎

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@@ -24,15 +24,21 @@
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package org.biojava.http;
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import static spark.Spark.*;
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import static spark.Spark.get;
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import org.biojava.http.routes.CESymmRoute;
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import org.biojava.http.routes.JsonTransformer;
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import org.biojava.http.routes.MMCIFRoute;
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import org.biojava.http.routes.NGLRoute;
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import org.biojava.http.routes.PDBRoute;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import spark.template.handlebars.HandlebarsTemplateEngine;
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public class ServerMain {
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public static Logger logger = LoggerFactory.getLogger(ServerMain.class);
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public static void main(String[] args) {
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// port(4567);
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@@ -43,5 +49,7 @@ public static void main(String[] args) {
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get(BioJavaRoutes.MMCIF, new MMCIFRoute());
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get(BioJavaRoutes.NGL, new NGLRoute(), new HandlebarsTemplateEngine());
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get(BioJavaRoutes.CESYMM_JSON, new CESymmRoute(),new JsonTransformer());
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}
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}

‎src/main/java/org/biojava/http/json/CESymmResultSerializer.java‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
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*
9+
* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
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*
18+
* http://www.biojava.org/
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*
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* Created on Jul 7, 2016
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* Author: blivens
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*
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*/
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package org.biojava.http.json;
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import java.lang.reflect.Type;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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import com.google.gson.JsonSerializationContext;
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import com.google.gson.JsonSerializer;
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public class CESymmResultSerializer implements JsonSerializer<CeSymmResult> {
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private static final Logger logger = LoggerFactory.getLogger(CESymmResultSerializer.class);
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@Override
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public JsonElement serialize(CeSymmResult src, Type typeOfSrc, JsonSerializationContext context) {
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logger.info("Serializing to json");
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JsonObject json = new JsonObject();
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json.addProperty("multipleAlignment", MultipleAlignmentWriter.toAlignedResidues(src.getMultipleAlignment()));
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json.addProperty("structureId",src.getStructureId().getIdentifier());
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json.addProperty("numRepeats", src.getNumRepeats());
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json.addProperty("refined", src.isRefined());
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return json;
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}
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}

‎src/main/java/org/biojava/http/routes/CESymmRoute.java‎

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@@ -25,7 +25,6 @@
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package org.biojava.http.routes;
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import org.biojava.http.BioJavaRoutes;
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import org.biojava.http.models.CESymmParams;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureIO;
@@ -35,21 +34,20 @@
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import spark.ModelAndView;
3937
import spark.Request;
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import spark.Response;
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import spark.TemplateViewRoute;
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import spark.Route;
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/**
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* Handle requests for {@link BioJavaRoutes#MMCIF}
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* @author Spencer Bliven
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*
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*/
48-
public class CESymmRoute implements TemplateViewRoute {
46+
public class CESymmRoute implements Route {
4947
public static Logger logger = LoggerFactory.getLogger(CESymmRoute.class);
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5149
@Override
52-
public ModelAndView handle(Request request, Response response) throws Exception {
50+
public CeSymmResult handle(Request request, Response response) {
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String id = request.params(":id");
5452
if(id == null) {
5553
response.status(404);
@@ -65,9 +63,7 @@ public ModelAndView handle(Request request, Response response) throws Exception
6563
}
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Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
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CeSymmResult result = CeSymm.analyze(ca);
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69-
CESymmParams params = new CESymmParams(result);
70-
return new ModelAndView(params, "cesymm.html.hbs");
66+
return result;
7167
} catch(Exception e) {
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logger.error("Error",e);
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response.status(404);

‎src/main/java/org/biojava/http/routes/JsonTransformer.java‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,51 @@
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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
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* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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* Created on Jul 6, 2016
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* Author: blivens
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*
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*/
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25+
package org.biojava.http.routes;
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27+
import org.biojava.http.json.CESymmResultSerializer;
28+
import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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30+
import spark.ResponseTransformer;
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32+
import com.google.gson.Gson;
33+
import com.google.gson.GsonBuilder;
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35+
public class JsonTransformer implements ResponseTransformer {
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37+
private Gson gson;
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39+
public JsonTransformer() {
40+
super();
41+
gson = new GsonBuilder()
42+
.registerTypeAdapter(CeSymmResult.class, new CESymmResultSerializer())
43+
.create();
44+
}
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46+
@Override
47+
public String render(Object model) {
48+
return gson.toJson(model);
49+
}
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51+
}

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

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Original file line numberDiff line numberDiff line change
@@ -2,13 +2,10 @@
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<html>
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<head>
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<meta charset='utf-8'>
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<title>CE-Symm Analysis of {{structureId}}</title>
5+
<title>{{structureId}}</title>
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</head>
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<body>
88

9-
<h1>CE-Symm Analysis of {{structureId}}</h1>
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<script src="{{url}}"></script>
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<script>

‎src/test/java/org/biojava/http/routes/TestJsonTransformer.java‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,60 @@
1+
/*
2+
* BioJava development code
3+
*
4+
* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
19+
*
20+
* Created on Jul 7, 2016
21+
* Author: blivens
22+
*
23+
*/
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25+
package org.biojava.http.routes;
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27+
import static org.junit.Assert.*;
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29+
import java.io.IOException;
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31+
import org.biojava.nbio.structure.Atom;
32+
import org.biojava.nbio.structure.Structure;
33+
import org.biojava.nbio.structure.StructureException;
34+
import org.biojava.nbio.structure.StructureIO;
35+
import org.biojava.nbio.structure.StructureTools;
36+
import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
37+
import org.biojava.nbio.structure.symmetry.internal.CeSymm;
38+
import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
39+
import org.junit.Test;
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41+
import com.google.gson.Gson;
42+
43+
public class TestJsonTransformer {
44+
45+
@Test
46+
public void testCeSymmResult() throws IOException, StructureException {
47+
Structure s = StructureIO.getStructure("1HIV.A");
48+
Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
49+
CESymmParameters params = new CESymmParameters();
50+
params.setSymmLevels(1);
51+
params.setOptimization(false);
52+
CeSymmResult result = CeSymm.analyze(ca);
53+
JsonTransformer trans = new JsonTransformer();
54+
String json = trans.render(result);
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56+
assertNotNull(json);
57+
System.out.println(json);
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}
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}

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