h1. How to test on productive server (temporary)

1. Go to https://openbis-csb.ethz.ch/openbis (all CISD developers have INSTANCE_ADMIN role assigned)
- there is a test experiment EXPERIMENT_TEST and a test sample SAMPLE_TEST with a few datasets.
- to keep the instance clean one should only:
-- create/delete samples attached to EXPERIMENT_TEST (don't delete sample SAMPLE_TEST)
-- register/delete datasets attached to test samples 
2. Login to bs-plasmids.ethz.ch as openbis 
3. There is a link 'dss-data' to a shared directory with a dropbox ('incoming') and an example
of a directory with files that can be registered as datasets for sample SAMPLE_TEST.
- to register datasets for the SAMPLE_TEST sample copy ~/dss-data/SAMPLE_TEST to ~/dss-data/incoming 

h1. Quick Setup for development mode

1. openbis 
1.1 in service.properties set: database.kind = plasmids
1.2 create a clean db using the script plasmid/resource/recreate_db.sh (change OWNER)

2. PlasMapper
2.1. unzip plasmid/resource/PlasMapper/jetty.zip
2.2. unzip plasmid/resource/PlasMapper/PlasMapper_dist.zip and move PlasMapper to webapps
2.3. Install blastall. Latest version can be downloaded from ftp://ftp.ncbi.nih.gov/blast/executables/release/LATEST.
2.3. change all paths leading to PlasMapper webapp dir and blastall in 
PlasMapper/WEB-INF/classes/ca/ualberta/xdong/plasMapper/annotate/plasMapConfiguration_en_CA.properties

3. plasmids
3.1 in targets create directories:
- targets/playground/data/incoming
- targets/playground/data/incoming-cifex
- targets/playground/data/store
3.2 change values of properties in /etc/service.properties needed for PlasMapper integration
main-thread.storage-processor.plasmapper-root-dir
main-thread.storage-processor.plasmapper-base-url

h1. Run and prepare data

1. run openbis
2. import samples using plasmid/resource/example/sample-import.tsv (multiple sample type)
3. run plasmid DSS using launch configuration from plasmid/resource/eclipse
4. run the external jetty with PlasMapper deployed
 
To test dataset registration and integration with PlasMapper copy an example directory 
plasmid/resource/example/FRP_1 to targets/playground/data/incoming. Datasets
will be attached to sample with code 'BOX_1:FRP_1'.