ECDP can be build and deployed on tomcat+mysql or you grab the docker version
for Docker: docker pull zackramjan/ecdp to start docker container: docker run -ti -d --privileged --name=ecdp_docker -v /sys/fs/cgroup:/sys/fs/cgroup:ro -p 8080:8080 ecdp (optionally you can add -p 3306:3306 if you want to connect to mariaDB/mysql)
to build: GXT4.0 GWT1.7 Java7 MariaDB
checkout, Gwt-compile, then deploy war dir to tomcat. make sure /ecdp/src/config.properties has your correct DB connection info.
to submit updates, use the following json syntax and post to addanalysis.jsp. note the the first 3 properties should be unique, but are not supplied by the system. you can use your internal LIMS ids or generate uuids if needed.
you can optionally include a file url for each metric, or if you just wish to associate files, you can skip metricName/Value for a given entry
{
"experimentID":"myExp564",
"sampleId":"ABC23",
"analysisID":"Run2_For_ABC455",
"metrics":[
{
"metricName":"Date_Sequenced",
"metricValue":"Jan 22 2016"
},
{
"metricName":"project",
"metricValue":"ABC project",
"metricFileName":"http://path-an-file.bam",
"metricFileSize":123123
},
{
"metricName":"sample_name",
"metricValue":"zacktest"
},
{
"metricFileName":"s3://asdasd.asdad/123123.bam",
"metricFileSize":123123
},
{
"metricName":"processing",
"metricValue":"nomeseq"
}
]
}
save your json to a file (ex: test.json) and upload to the server with curl: curl -H "Content-Type: application/json" -X POST -d @test.json http://www.ecdp.org/addanalysis.jsp
changes are initially stored in an intermediate table, to push to the main table for diplsay on the web: curl http://www.ecdp.org/updatedb.jsp
to delete an analysis curl --data "analysis_id=Run2_For_ABC455" http://www.ecdp.org/deleteanalysis.jsp