diff --git a/test-data/screening/readme.mdown b/test-data/screening/readme.mdown new file mode 100644 index 0000000000000000000000000000000000000000..11e2fa05e786d5ad9ac329e367bfc41d8063b189 --- /dev/null +++ b/test-data/screening/readme.mdown @@ -0,0 +1,65 @@ +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 + * 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.py + * A python script that generates raw-images for a plate. It can be configured, by modifying the source, to generate time and/or depth points and produce merged (RGB) or split (R, G, B in separate files) files. + * Later, this will be expanded to produce overlay images as well + * running generate-test-plate.py will produce a folder named PLATONIC containing images in the current directory + * n.b. This script will only run on MacOS 10.5+ + +Use +=== + +Follow these instructions to use this infrastructure. It instructions assume that the screening version of openBIS has been installed, but, not necessarily started. + +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 openBIS +----------------- + +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 + +Start openBIS +------------- + +1. Start openBIS and DSS and log in as admin/admin. +2. Create a plate sample called (you can call it PLATONIC if you want) with an 8x12 geometry. + +Generate and Register Plate +-------------- + +Run the generate-test-plate.py script. If your plate is not called PLATONIC, you will need to rename the folder to the name of your plate. Put the folder with the images into the incoming-platonic dropbox. + +View the plate in openBIS; you should see the images you registered.