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sblivensbliven
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Refactoring
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11 files changed

+390
-144
lines changed

11 files changed

+390
-144
lines changed

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

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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
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* be distributed with the code. If you do not have a copy,
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* see:
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*
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* 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,
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* 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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package org.biojava.http;
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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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}

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

Lines changed: 15 additions & 2 deletions
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@@ -26,9 +26,22 @@
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import static spark.Spark.*;
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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 spark.template.handlebars.HandlebarsTemplateEngine;
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public class ServerMain {
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public static void main(String[] args) {
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// port(5678); <- Uncomment this if you want spark to listen to port 5678 in stead of the default 4567
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get("/hello", (request, response) -> "Hello World!");
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// port(4567);
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get("/", (r,r2) -> "BioJava HTTP");
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get(BioJavaRoutes.PDB, new PDBRoute());
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get(BioJavaRoutes.MMCIF, new MMCIFRoute());
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get(BioJavaRoutes.NGL, new NGLRoute(), new HandlebarsTemplateEngine());
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}
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}

src/main/java/org/biojava/http/structure/CESymmParams.java renamed to src/main/java/org/biojava/http/models/CESymmParams.java

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@@ -22,7 +22,7 @@
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*
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*/
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package org.biojava.http.structure;
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package org.biojava.http.models;
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
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src/main/java/org/biojava/http/structure/NGLParams.java renamed to src/main/java/org/biojava/http/models/NGLParams.java

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*
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*/
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package org.biojava.http.structure;
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package org.biojava.http.models;
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public class NGLParams {
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private String url;

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

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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+
*
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* 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,
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* 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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package org.biojava.http.models;
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public class NGLRouteParams extends NGLParams{
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private String structureId;
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public NGLRouteParams(String structureId,String structUrl) {
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super(structUrl);
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this.structureId = structureId;
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}
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public String getStructureId() {
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return structureId;
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}
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public void setStructureId(String structureId) {
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this.structureId = structureId;
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}
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}

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

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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
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*
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,
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* or to join the biojava-l mailing list, visit the home page
16+
* 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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package org.biojava.http.routes;
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import org.biojava.http.BioJavaRoutes;
28+
import org.biojava.http.models.CESymmParams;
29+
import org.biojava.nbio.structure.Atom;
30+
import org.biojava.nbio.structure.Structure;
31+
import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.StructureTools;
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import org.biojava.nbio.structure.symmetry.internal.CeSymm;
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import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
35+
import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import spark.ModelAndView;
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import spark.Request;
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import spark.Response;
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import spark.TemplateViewRoute;
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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 {
49+
public static Logger logger = LoggerFactory.getLogger(CESymmRoute.class);
50+
51+
@Override
52+
public ModelAndView handle(Request request, Response response) throws Exception {
53+
String id = request.params(":id");
54+
if(id == null) {
55+
response.status(404);
56+
logger.error("null id");
57+
return null;
58+
}
59+
try {
60+
Structure s = StructureIO.getStructure(id);
61+
if(s == null) {
62+
response.status(404);
63+
logger.error("null structure for "+id);
64+
return null;
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}
66+
Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
67+
CeSymmResult result = CeSymm.analyze(ca);
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69+
CESymmParams params = new CESymmParams(result);
70+
return new ModelAndView(params, "cesymm.html.hbs");
71+
} catch(Exception e) {
72+
logger.error("Error",e);
73+
response.status(404);
74+
return null;
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}
76+
}
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78+
}

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

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/*
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* BioJava development code
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*
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 6, 2016
21+
* Author: blivens
22+
*
23+
*/
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25+
package org.biojava.http.routes;
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27+
import org.biojava.http.BioJavaRoutes;
28+
import org.biojava.nbio.structure.Structure;
29+
import org.biojava.nbio.structure.StructureException;
30+
import org.biojava.nbio.structure.StructureIO;
31+
import org.slf4j.Logger;
32+
import org.slf4j.LoggerFactory;
33+
34+
import spark.Request;
35+
import spark.Response;
36+
import spark.Route;
37+
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/**
39+
* Handle requests for {@link BioJavaRoutes#MMCIF}
40+
* @author Spencer Bliven
41+
*
42+
*/
43+
public class MMCIFRoute implements Route {
44+
public static Logger logger = LoggerFactory.getLogger(MMCIFRoute.class);
45+
46+
@Override
47+
public String handle(Request request, Response response) throws Exception {
48+
String id = request.params(":id");
49+
if(id == null) {
50+
response.status(404);
51+
return "No structure specified";
52+
}
53+
try {
54+
Structure s = StructureIO.getStructure(id);
55+
if(s == null) {
56+
response.status(404);
57+
return "Error fetching "+id;
58+
}
59+
String pdb = s.toMMCIF();
60+
String filename = id+".cif";
61+
response.header("Content-Type", "chemical/x-pdb");
62+
response.header("Content-Disposition", String.format("inline; filename=\"%s\"",filename));
63+
return pdb;
64+
} catch(StructureException e) {
65+
logger.error("Error",e);
66+
response.status(404);
67+
return "Error fetching "+id;
68+
}
69+
}
70+
71+
}

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

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,64 @@
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 6, 2016
21+
* Author: blivens
22+
*
23+
*/
24+
25+
package org.biojava.http.routes;
26+
27+
import org.biojava.http.BioJavaRoutes;
28+
import org.biojava.http.models.NGLRouteParams;
29+
import org.slf4j.Logger;
30+
import org.slf4j.LoggerFactory;
31+
32+
import spark.ModelAndView;
33+
import spark.Request;
34+
import spark.Response;
35+
import spark.TemplateViewRoute;
36+
37+
/**
38+
* Handle requests for {@link BioJavaRoutes#MMCIF}
39+
* @author Spencer Bliven
40+
*
41+
*/
42+
public class NGLRoute implements TemplateViewRoute {
43+
public static Logger logger = LoggerFactory.getLogger(NGLRoute.class);
44+
45+
@Override
46+
public ModelAndView handle(Request request, Response response) throws Exception {
47+
String id = request.params(":id");
48+
if(id == null) {
49+
response.status(404);
50+
logger.error("null id");
51+
return null;
52+
}
53+
try {
54+
String structUrl = BioJavaRoutes.MMCIF.replace(":id", id);
55+
NGLRouteParams params = new NGLRouteParams(id,structUrl);
56+
return new ModelAndView(params, "ngl.html.hbs");
57+
} catch(Exception e) {
58+
logger.error("Error",e);
59+
response.status(404);
60+
return null;
61+
}
62+
}
63+
64+
}

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