Rapid prototyping of a read-only Lims using JSON and Apache Velocity.

In a previous post, I showed how to use the Apache Velocity template engine to format JSON data.



Since that post, I've moved my application to a github repository: https://github.com/lindenb/jsvelocity. The project contains a java-based standalone tool to process the JSON data.
Here is an example: The JSON data:

{
individuals:[
    {
    name: "Riri",
    age: 8,
    duck: true
    },
    {
    name: "Fifi",
    age: 9,
    duck: true
    },
    {
    name: "Loulou",
    age: 10,
    duck: true
    }
    ]
}

.... and the velocity template:

#foreach($indi in ${all.individuals})
<h1>${indi['name']}</h1>
Age:${indi.age}<br/>${indi.duck}
#end

... with the following command line ...

$ java -jar dist/jsvelocity.jar \
    -f all test.json \
    test.vm

... produces the following output ...

<h1>Riri</h1>
Age:8<br/>true
<h1>Fifi</h1>
Age:9<br/>true
<h1>Loulou</h1>
Age:10<br/>true

Today I wrote a web version of the tool using the jetty server. I wanted to quickly write a web interface to display various summaries for our NGS experiments.
My JSON input looks like this:

{
"sequencer":[
 {
 "name":"HiSeq"
 },
 {
 "name":"MiSeq"
 }
 ],
"run":[ {
 "sequencer":"HiSeq",
 "flowcell":"C2AVTACXX",
 "name":"131010_C2AVTACXX_61",
 "date":"2013-10-10",
 "comment":"A comment",
 "samples":[
  {
  "name":"CD0001",
  "meancov": 10
  },
  {
  "name":"CD0002",
  "meancov": 20.0
  }
  ,
  {
  "name":"CD0003",
  "meancov": 30.0
  }
  ]
 },
 {
 "sequencer":"MiSeq",
 "flowcell":"C3VATACYY",
 "name":"131011_C3VATACYY_62",
 "date":"2013-10-11",
 "comment":"Another comment",
 "samples":[
  {
  "name":"CD0001",
  "meancov": 11
  },
  {
  "name":"CD0006",
  "meancov": 21.0
  }
  ,
  {
  "name":"CD0008",
  "meancov": null
  }
  ]
 },
 {
 "sequencer":"MiSeq",
 "flowcell":"C4VATACYZ",
 "name":"131012_C4VATACYZ_63",
 "date":"2013-10-12",
 "comment":"Another comment",
 "samples":[
  {
  "name":"CD0010",
  "meancov":1,
  "comment":"Failed, please, re-sequence"
  }
  ]
 }
 
 
 ],
"samples":[ 
 { "name":"CD0001" },
 { "name":"CD0002" },
 { "name":"CD0003" }, 
 { "name":"CD0004" }, 
 { "name":"CD0005" }, 
 { "name":"CD0006" }, 
 { "name":"CD0007" }, 
 { "name":"CD0008" },
 { "name":"CD0009" },
 { "name":"CD0010" }
 ],
"projects":[
 {
 "name":"Disease1",
 "description": "sequencing Project 1",
 "samples":["CD0001","CD0002","CD0006","CD0009"]
 },
 {
 "name":"Disease2",
 "description": "sequencing Project 2",
 "samples":["CD0002","CD0003","CD0008","CD0009"]
 }
 ]

}

One velocity template is used to browse this 'database': https://github.com/lindenb/jsvelocity/blob/master/src/test/resources/velocity/lims.vm.
The server is started like:

java -jar dist/webjsvelocity.jar  \
    -F lims src/test/resources/json/lims.json \
    src/test/resources/velocity/lims.vm

2013-10-17 12:43:35.566:INFO:oejs.Server:main: jetty-9.1.0.M0
2013-10-17 12:43:35.602:INFO:oejs.ServerConnector:main: Started ServerConnector@72dcb6{HTTP/1.1}{0.0.0.0:8080}
(...)

And here is a screenshot of the result:






That's it,

Pierre