A couchdb-like application using apache JETTY and BerkeleyDB. My notebook
This is my notebook for the Jetty API. Jetty provides an Web server and javax.servlet container. It can be embedded in devices, tools, frameworks, application servers, and clusters. I find it more easier for developping and testing a new web application as it doesn't require some deployement descriptors, some configuration files, a web container, etc... like in apache tomcat. As I will show below, a whole web applications can be embedded in a single java class.
As an example, I wrote a couchdb-like web application, named DivanDB ('divan' is the french word for couch), using Jetty and Berkeleydb. The source file is available on github at:(See also my previous post :CouchDB for Bioinformatics: Storing SNPs - My Notebook)
The BerkeleyDB-base key/value datastore
The class BDBStorage consists in a BerkeleyDB environment and a BerkeleyDB database. The database stores keys and the values as String./** a berkeley-db String/String datastore */
private static class BDBStorage
{
/** bdb environment */
private Environment environment=null;
/** string/string database */
private Database database=null;
private BDBStorage()
{
}
/** open environment & database */
private void open(File dbHome) throws DatabaseException
{
(...)
}
/** close environment & database */
private void close()
{
(...)
}
}
The web context
A servlet context is created where we put a BDBStorage. We also tell the context about the DivanDB servlet and the path of the application.
DivanDB app=new DivanDB();
BDBStorage storage=new BDBStorage();
ServletContextHandler context = new ServletContextHandler();
context.setAttribute(STORAGE_ATTRIBUTE, storage);
context.addServlet(new ServletHolder(app),"/*");
context.setContextPath("/divandb");
context.setResourceBase(".");
The server
The embedded server listens to the specified port. We add the context to the server, it is started and listen to the queries forever./* create a new server */
Server server = new Server(port);
/* context */
server.setHandler(context);
/* start server */
server.start();
/* loop forever */
server.join();
The Servlet
The servlet DivanDB receives the POST, GET and DELETE queries just like couchdb. It decodes the JSON data using a JSON API provided in the jetty distribution. See the code for more information.Start the server
$java -jar dist/divandb.jar
2011-06-19 18:12:16.823:INFO::jetty-8.0.0.M3
2011-06-19 18:12:16.896:INFO::Started SelectChannelConnector@0.0.0.0:8080 STARTING
Testing, using CURL
Add a single snp. Here the id is a concatenation of the chromosome number and the genomic position:$curl -X PUT -d '{"id":"010000011390","name":"rs75100478","avHet":0.5,"chrom":"chr1","position":11390}' http://localhost:8080/divandb/
{"ok":"true","id":["010000011390"]}Add single snp without id (it will be generated):$curl -X PUT -d '{"name":"rs3877545","avHet":0.375,"chrom":"chr1","position":11507}' http://localhost:8080/divandb/
{"ok":"true","id":["id972755720"]}Add an array of SNPs:$ curl -X PUT -d '[{"id":"010000011390","name":"rs75100478","avHet":0.5,"chrom":"chr1","position":11390},{"id":"010000011507","name":"rs3877545","avHet":0.375,"chrom":"chr1","position":11507},{"id":"010000011863","name":"rs76933399","avHet":0.46875,"chrom":"chr1","position":11863},{"id":"010000011920","name":"rs78105014","avHet":0.5,"chrom":"chr1","position":11920},{"id":"010000011959","name":"rs71234145","avHet":0.5,"chrom":"chr1","position":11959},{"id":"010000012048","name":"rs7357889","avHet":0.277778,"chrom":"chr1","position":12048},{"id":"010000012073","name":"rs76972523","avHet":0.5,"chrom":"chr1","position":12073},{"id":"010000012120","name":"rs78253371","avHet":0.5,"chrom":"chr1","position":12120},{"id":"010000012148","name":"rs78371031","avHet":0.5,"chrom":"chr1","position":12148},{"id":"010000012158","name":"rs79313092","avHet":0.5,"chrom":"chr1","position":12158},{"id":"010000012168","name":"rs74400200","avHet":0.5,"chrom":"chr1","position":12168},{"id":"010000012169","name":"rs79903148","avHet":0.375,"chrom":"chr1","position":12169},{"id":"010000012213","name":"rs79272378","avHet":0.5,"chrom":"chr1","position":12213},{"id":"010000012264","name":"rs2475482","avHet":0.444444,"chrom":"chr1","position":12264},{"id":"010000012295","name":"rs76096671","avHet":0.375,"chrom":"chr1","position":12295},{"id":"010000012295","name":"rs79461972","avHet":0.375,"chrom":"chr1","position":12295},{"id":"010000012305","name":"rs71236994","avHet":0.5,"chrom":"chr1","position":12305},{"id":"010000012332","name":"rs2981846","avHet":0.375,"chrom":"chr1","position":12332},{"id":"010000012336","name":"rs76760687","avHet":0.375,"chrom":"chr1","position":12336},{"id":"010000012355","name":"rs76588012","avHet":0.444444,"chrom":"chr1","position":12355}]' http://localhost:8080/divandb/
{"ok":"true","id":["010000011390","010000011507","010000011863","010000011920","010000011959","010000012048","010000012073","010000012120","010000012148","010000012158","010000012168","010000012169","010000012213","010000012264","010000012295","010000012295","010000012305","010000012332","010000012336","010000012355"]Deleting a SNP:$curl -X DELETE -d '{"id":"2065420809"}' http://localhost:8080/divandb/
{"ok":"true","id":["id972755720"]}
List all the SNPs:$ curl http://localhost:8080/divandb/List the SNPs on chr1 between 12000 and 12150:
[
{"position":11390,"id":"010000011390","_timestamp":"1308501619331","name":"rs75100478","avHet":0.5,"chrom":"chr1"},
{"position":11507,"id":"010000011507","_timestamp":"1308501619335","name":"rs3877545","avHet":0.375,"chrom":"chr1"},
{"position":11863,"id":"010000011863","_timestamp":"1308501619336","name":"rs76933399","avHet":0.46875,"chrom":"chr1"},
{"position":11920,"id":"010000011920","_timestamp":"1308501619336","name":"rs78105014","avHet":0.5,"chrom":"chr1"},
{"position":11959,"id":"010000011959","_timestamp":"1308501619337","name":"rs71234145","avHet":0.5,"chrom":"chr1"},
{"position":12048,"id":"010000012048","_timestamp":"1308501619337","name":"rs7357889","avHet":0.277778,"chrom":"chr1"},
{"position":12073,"id":"010000012073","_timestamp":"1308501619338","name":"rs76972523","avHet":0.5,"chrom":"chr1"},
{"position":12120,"id":"010000012120","_timestamp":"1308501619338","name":"rs78253371","avHet":0.5,"chrom":"chr1"},
{"position":12148,"id":"010000012148","_timestamp":"1308501619339","name":"rs78371031","avHet":0.5,"chrom":"chr1"},
{"position":12158,"id":"010000012158","_timestamp":"1308501619339","name":"rs79313092","avHet":0.5,"chrom":"chr1"},
{"position":12168,"id":"010000012168","_timestamp":"1308501619339","name":"rs74400200","avHet":0.5,"chrom":"chr1"},
{"position":12169,"id":"010000012169","_timestamp":"1308501619340","name":"rs79903148","avHet":0.375,"chrom":"chr1"},
{"position":12213,"id":"010000012213","_timestamp":"1308501619340","name":"rs79272378","avHet":0.5,"chrom":"chr1"},
{"position":12264,"id":"010000012264","_timestamp":"1308501619341","name":"rs2475482","avHet":0.444444,"chrom":"chr1"},
{"position":12295,"id":"010000012295","_timestamp":"1308501619342","name":"rs79461972","avHet":0.375,"chrom":"chr1"},
{"position":12305,"id":"010000012305","_timestamp":"1308501619344","name":"rs71236994","avHet":0.5,"chrom":"chr1"},
{"position":12332,"id":"010000012332","_timestamp":"1308501619348","name":"rs2981846","avHet":0.375,"chrom":"chr1"},
{"position":12336,"id":"010000012336","_timestamp":"1308501619348","name":"rs76760687","avHet":0.375,"chrom":"chr1"},
{"position":12355,"id":"010000012355","_timestamp":"1308501619349","name":"rs76588012","avHet":0.444444,"chrom":"chr1"}
]
$ curl "http://localhost:8080/divandb/?startkey=010000012000&endkey=010000012150"
[
{"position":12048,"id":"010000012048","_timestamp":"1308501619337","name":"rs7357889","avHet":0.277778,"chrom":"chr1"},
{"position":12073,"id":"010000012073","_timestamp":"1308501619338","name":"rs76972523","avHet":0.5,"chrom":"chr1"},
{"position":12120,"id":"010000012120","_timestamp":"1308501619338","name":"rs78253371","avHet":0.5,"chrom":"chr1"},
{"position":12148,"id":"010000012148","_timestamp":"1308501619339","name":"rs78371031","avHet":0.5,"chrom":"chr1"}
]
List 3 SNPs starting from index=2
$ curl "http://localhost:8080/divandb/?start=2&limit=3"
[
{"position":11507,"id":"010000011507","_timestamp":"1308501619335","name":"rs3877545","avHet":0.375,"chrom":"chr1"},{"position":11863,"id":"010000011863","_timestamp":"1308501619336","name":"rs76933399","avHet":0.46875,"chrom":"chr1"},
{"position":11920,"id":"010000011920","_timestamp":"1308501619336","name":"rs78105014","avHet":0.5,"chrom":"chr1"}
]
That's it
Pierre
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