screeningBee Data Analysis Tools

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====== Installing a Webapp in OpenBIS STAGE ======

**(1)** Download the simple example ''service-demo.zip'' from https://wiki-bsse.ethz.ch/download/attachments/101197296/service-demo.zip?version=1&modificationDate=1380265520019

**(2)** Unzip it in the core plugins folder:
<code>
# ~/stage/openBIS/servers/core-plugins> unzip service-demo.zip 
</code>

**(3)** Enable the new core plugin by editing the ''core-plugins.propeties'' file:
<code>
# ~/stage/openBIS/servers/core-plugins> vi core-plugins.properties  
</code>
Once edited this file has the following content:
<code>
enabled-modules = screening, service-demo

#disabled-core-plugins = screening:
disabled-core-plugins = screening:data-sources, screening:drop-boxes, screening:image-overview-plugins, screening:maintenance-tasks, screening:services, screening:dss-data-sources
</code>

**(4)** Restart openBIS:
<code>
#  ~/stage/openBIS/servers/openBIS-server/jetty/logs> alldown.sh 
Stopping Data Store Server (not running - nothing to do)
Shutting openBIS down...
#  ~/stage/openBIS/servers/openBIS-server/jetty/logs> allup.sh 
Starting openBIS...
.........Done.
Starting Data Store Server (pid 5918)
</code>
Info: During openBIS start, two new symlinks are created in the jetty webapp directory pointing to the two new installed wepapps from the "service-demo" example:
<code>
#  ~/stage/openBIS/servers/openBIS-server/jetty/webapps/openbis/webapp> ls -al
total 16
drwxr-xr-x 2 mx_nas mx-servers 4096 Oct  2 12:28 .
drwxr-xr-x 9 mx_nas mx-servers 4096 Aug 20 17:41 ..
lrwxrwxrwx 1 mx_nas mx-servers  118 Oct  2 12:28 aggregation -> /home/openbis/stage/openBIS/servers/openBIS-server/jetty/../../core-plugins/service-demo/1/as/webapps/aggregation/html
lrwxrwxrwx 1 mx_nas mx-servers  116 Oct  2 12:28 ingestion -> /home/openbis/stage/openBIS/servers/openBIS-server/jetty/../../core-plugins/service-demo/1/as/webapps/ingestion/html
</code>

**(5)** Adapt ''webapp.js'':
<code>
#  ~/stage/openBIS/servers/core-plugins/service-demo/1/as/webapps/aggregation/html> vi webapp.js
#  ~/stage/openBIS/servers/core-plugins/service-demo/1/as/webapps/ingestion/html> vi webapp.js
</code>
What to adapt:
  * The openBIS server we use for our data.\\
In our case the hostname is ''infectx-stage.biozentrum.unibas.ch'':
<code>
openbisServer = new openbis('https://infectx-stage.biozentrum.unibas.ch/openbis/openbis', 'https://infectx-stage.biozentrum.unibas.ch/datastore_server');
</code>
  * The DSS (data source) to contact. 
To find out what the code of the data source is, either have a look at the ''service.properties'' of the data store server, (key: ''data-store-server-code = DSS1''), or have a look at the openbis DB calling ''<openBIS_DB>=# select code from data_stores;''\\
In our case tha value is ''dss-screening'':
<code>
openbisServer.createReportFromAggregationService("dss-screening", "example-aggregation-service", parameters, displayReturnedTable);
</code>


**(6)** For the ingestion service, adapt the ''script.py'' script which registers a new sample into openBIS:
<code>
#  ~/stage/openBIS/servers/core-plugins/service-demo/1/dss/reporting-plugins/example-ingestion-service> vi script.py
</code>

It is necessary to set an existing experiment and sample type.\\
In our case we set as experiment ''/BEE/VACCINIA_TEAM/VACCINIA-DU-K1'' and as sample type ''CONTROL_WELL'':
<code>
  sampleId = "/BEE/" + sampleCode
  sample = tr.createNewSample(sampleId, "CONTROL_WELL")
  exp = tr.getExperiment("/BEE/VACCINIA_TEAM/VACCINIA-DU-K1")
  sample.setExperiment(exp)
</code>


**(7)** The wepapps can be accessed at the URLs:\\
''https://infectx-stage.biozentrum.unibas.ch/openbis/webapp/aggregation/''\\
''https://infectx-stage.biozentrum.unibas.ch/openbis/webapp/ingestion/''

====== Calling external libraries from Jython script ======
**1.** The lib should go into folder where the Jython script resides. Simply create a ''lib'' folder and put all jars inside. \\
Here is an example:
<code>
# ~/openbis_example_wepapp/servers/core-plugins/appExample/1/dss/reporting-plugins/apiExample> ll lib/

total 17104
drwxr-xr-x  7 kohleman  staff      238 Oct  9 17:23 ./
drwxr-xr-x  6 kohleman  staff      204 Oct  9 17:25 ../
-rw-r--r--@ 1 kohleman  staff   168586 Sep 27 14:34 cisd-hcscld.jar
-rw-r--r--@ 1 kohleman  staff  1252347 Sep 27 14:34 cisd-jhdf5-core.jar
-rw-r--r--@ 1 kohleman  staff  2852257 Sep 27 14:34 hdf5-linux-intel.jar
-rw-r--r--@ 1 kohleman  staff  2652865 Sep 27 14:34 hdf5-macosx-intel.jar
-rw-r--r--@ 1 kohleman  staff  1821318 Sep 27 14:34 hdf5-windows-intel.jar
</code>

**2.** Then restart openBIS. This creates links in the ''dss/lib'' folder to those jars. For old version, this doesn't happen and the jars should be copied there directly.

**3.** In the jython script use the import command, for example:
<code>
from ch.ethz.sis.hcscld import CellLevelDataset
</code>
The * star does not work, you have to import each class separately.

**4.** And that is it!  Use Java from Jython as in any other case.
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