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
