Screening Test Data
===================

This folder contains scripts and other files for creating and curating data for a screening instance of openBIS.

Manifest
========

* config 
 	* openbis and dss system.properties files for a local instance of openbis

* etc 
	* data-set-handler-microscope.py -- A python drop-box that imports microscopy images

	* data-set-handler-features.py -- A python drop-box that imports feature vectors

	* data-set-handler-splitted.py -- A python drop-box that imports plates comprised multiple single-channel images

	* data-set-handler-plate.py -- A python drop-box script for dss that imports plates and analysis data

* source
	* admin-console
		* An admin-console script that creates optional meta-data for the screening test data. 
		  Running this script is not required.

	* bash
		* create-empty-screening-db.sh
			* A script that initializes an empty screening database. This must be run to create the initial 
			  database for the test data if no database exists.
			
	* python
		* generate-test-plate-analysis.py -- A script that generates analysis data (csv files)

		* generate-test-plate-overlays.py -- A script that generates overlay-images for a plate
			* n.b. This script will only run on MacOS 10.5+			

		* generate-test-plate.py -- A script that generates raw-images for a plate. This can be
		  colorful images or black-and-white images for each channel.
			* n.b. This script will only run on MacOS 10.5+

		* generate-test-series.py -- A script that generates a microscopy image series
			* n.b. This script will only run on MacOS 10.5+	
			
			
* exp-1-library.xls
  An Excel file for importing a library (defining materials and plates) to be uploaded by
  menu item "Administration -> General Import"	

Use
===

Follow these instructions to use this infrastructure. It instructions assume that 
the screening version of openBIS is running inside Eclipse.

Initialize DB
-------------

Run the initialization script.

> screening/source/bash/create-empty-screening-db.sh

This will create an initial screening database with the name used by the configuration files.

Configure Servers
-----------------

1. Replace the openBIS service.properties with screening/config/openbis-service.properties
2. Replace the dss service.properties with screening/config/dss-service.properties
3. In the screening folder create the following sub-folders 
* targets/platonic
* targets/platonic/store
* targets/platonic/incoming-platonic-microscope
* targets/platonic/incoming-platonic-plate
* targets/platonic/incoming-platonic-plate-features
* targets/platonic/incoming-platonic-plate-overlays
* targets/platonic/incoming-platonic-plate-splitted

Configure openBIS
-----------------

1. Start openBIS and DSS and log in as admin/admin.
2. Create space PLATONIC.
3. Create project SCREENING-EXAMPLES.
3. Create an experiment EXP-1 of type HCS_PLATONIC in this project.
4. Use the Import->General Import to import the file screening/exp-1-library.xls

Generate and Register Data
--------------------------

Run the script screening/source/bash/generate-test-experiment.sh to generate data for the experiment.

6. Register

* PLATE-1 -> targets/platonic/incoming-platonic-plate
* PLATE-1.OVERLAY-1 -> targets/platonic/incoming-platonic-plate-overlays
* PLATE-1.OVERLAY-2 -> targets/platonic/incoming-platonic-plate-overlays
* PLATE-1.analysis1.csv -> targets/platonic/incoming-platonic-plate-features
* PLATE-1.analysis2.csv -> targets/platonic/incoming-platonic-plate-features