# Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = dss-screening-platonic

# host name of the machine on which the datastore server is running
host-address = http://localhost

# parent directory of the store directory and all the dropboxes
root-dir = targets/platonic

# The root directory of the data store
storeroot-dir = ${root-dir}/store

# The directory for the python scripts (and other configuration data)
python-script-folder = ../test-data/screening/etc

# The directory where the command queue file is located; defaults to storeroot-dir 
commandqueue-dir =

# Create any incoming directories that do not already exist
incoming-dir-create = true

# Port
port = 8889
use-ssl = false

# Session timeout in minutes
session-timeout = 30

# Path to the keystore
keystore.path = dist/etc/openBIS.keystore
# Password of the keystore
keystore.password = changeit
# Key password of the keystore
keystore.key-password = changeit

# The check interval (in seconds)
check-interval = 5

# The time-out for clean up work in the shutdown sequence (in seconds).
# Note that that the maximal time for the shutdown sequence to complete can be as large 
# as twice this time.
# Remark: On a network file system, it is not recommended to turn this value to something 
# lower than 180.
shutdown-timeout = 2

# If free disk space goes below value defined here, a notification email will be sent.
# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
# specified or if value is negative, the system will not be watching.
highwater-mark = 1000

# If a data set is successfully registered it sends out an email to the registrator. 
# If this property is not specified, no email is sent to the registrator. This property
# does not affect the mails which are sent, when the data set could not be registered.
notify-successful-registration = false

# The URL of the openBIS server
server-url = ${host-address}:8888

# The username to use when contacting the openBIS server
username = etlserver

# The password for the etlserver user who contacts the openBIS server
password = etlserver_password

# The base URL for Web client access to the data store server.
download-url = ${host-address}:8889

# SMTP properties (must start with 'mail' to be considered).
# The current configuration saves the emails in the file system in the root directory 
mail.smtp.host = file://${root-dir}/emails
# mail.smtp.host = localhost
# mail.from = datastore_server@ethz.ch
# mail.smtp.user = 
# mail.smtp.password = 

core-plugins-folder = ../screening/source/core-plugins
enabled-technologies = screening

imaging-database.kind = platonic
screening-sql-root-folder = source/

# ---------------------------------------------------------------------------
# (optional) archiver configuration
# ---------------------------------------------------------------------------

# Configuration of an archiver task. All properties are prefixed with 'archiver.'.

# Archiver class specification (together with the list of packages this class belongs to).
#archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver

# ---------------------------------------------------------------------------
#                      INTERNAL CONFIGURATION, 
# Do not change this part unless you are developing openBIS extensions.
# ---------------------------------------------------------------------------

# ---------------------------------------------------------------------------
# screening database specification
# ---------------------------------------------------------------------------

data-sources = path-info-db

# Data source for pathinfo database
path-info-db.version-holder-class = ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
path-info-db.databaseEngineCode = postgresql
path-info-db.basicDatabaseName = pathinfo
path-info-db.databaseKind = platonic
path-info-db.scriptFolder = ../datastore_server/source/sql

# ---------------------------------------------------------------------------
# reporting and processing plugins configuration
# ---------------------------------------------------------------------------

# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
reporting-plugins =  well-image-analysis-graph, csv-viewer

well-image-analysis-graph.label = Image Analysis Graphs
well-image-analysis-graph.dataset-types = HCS_ANALYSIS_WELL_FEATURES
well-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisGraphReportingPlugin
well-image-analysis-graph.servlet-path = analysis_graph/
well-image-analysis-graph.properties-file = ${python-script-folder}/analysis-graph.properties
well-image-analysis-graph.servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet
well-image-analysis-graph.servlet.path = /${well-image-analysis-graph.servlet-path}*
well-image-analysis-graph.servlet.properties-file = ${well-image-analysis-graph.properties-file}

csv-viewer.label = CSV View 
csv-viewer.dataset-types = HCS_IMAGE_ANALYSIS_DATA
csv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
csv-viewer.separator = ,


# ---------------------------------------------------------------------------

maintenance-plugins = path-info-deletion, post-registration
path-info-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
path-info-feeding.execute-only-once = true

# Maintenance task for deleting entries in pathinfo database after deletion of data sets
path-info-deletion.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
path-info-deletion.interval = 120
path-info-deletion.data-source = path-info-db
path-info-deletion.data-set-perm-id = CODE
path-info-deletion.data-set-table-name = data_sets

# Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database  
post-registration.class = ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask
post-registration.interval = 30
post-registration.cleanup-tasks-folder = targets/cleanup-tasks
# The following date should the day when the DDS is started up the first time with PathInfoDatabaseFeedingTask.
# After PathInfoDatabaseFeedingTask has been performed it can be removed and the following line can be deleted.
#post-registration.ignore-data-sets-before-date = 2011-04-18
post-registration.last-seen-data-set-file = targets/last-seen-data-set
post-registration.post-registration-tasks = pathinfo-feeding
post-registration.pathinfo-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask


# ---------------------------------------------------------------------------
#                      DROPBOXES CONFIGURATION 
# ---------------------------------------------------------------------------

incoming-root-dir = ${root-dir}

# Globally used separator character which separates entities in a data set file name 
data-set-file-name-entity-separator = _

# The period of no write access that needs to pass before an incoming data item is considered 
# complete and ready to be processed (in seconds) [default: 300]. 
# Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
quiet-period=10

# code of the default space in openBIS to which the data will be imported
import-space-code = PLATONIC

# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
inputs= platonic-plate, platonic-plate-splitted, platonic-plate-overlay, platonic-plate-features, platonic-plate-series, platonic-microscope

# ---------------------------------------------------------------------------
# ---  platonic-plate  ------------------------------------------------------
# ---------------------------------------------------------------------------

# The dropbox for idealized data -- data that doesn't represent real screens, 
# rather data used for testing purposes
platonic-plate.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate
platonic-plate.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
platonic-plate.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
platonic-plate.script-path = ${python-script-folder}/data-set-handler-plate.py
platonic-plate.staging-dir = ${incoming-root-dir}

platonic-plate.storage-processor = ch.systemsx.cisd.etlserver.DispatcherStorageProcessor
platonic-plate.storage-processor.processors = images, analysis
# --- images - accepts all image datasets registrations
platonic-plate.storage-processor.images = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
platonic-plate.storage-processor.images.data-source = imaging-db
# --- analysis - accepts all other datasets (and assumes they are single CSV files)
platonic-plate.storage-processor.analysis = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
platonic-plate.storage-processor.analysis.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
platonic-plate.storage-processor.analysis.data-source = imaging-db
platonic-plate.storage-processor.analysis.separator = ,
platonic-plate.storage-processor.analysis.well-name-row = Well
platonic-plate.storage-processor.analysis.well-name-col = Well
platonic-plate.storage-processor.analysis.well-name-col-is-alphanum = true

platonic-plate-splitted. = platonic-plate.
platonic-plate-splitted.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate-splitted
platonic-plate-splitted.script-path = ${python-script-folder}/data-set-handler-plate-splitted.py

platonic-plate-overlay. = platonic-plate.
platonic-plate-overlay.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate-overlays
platonic-plate-overlay.script-path = ${python-script-folder}/data-set-handler-plate-overlays.py

platonic-plate-features. = platonic-plate.
platonic-plate-features.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate-features
platonic-plate-features.script-path = ${python-script-folder}/data-set-handler-plate-features.py

platonic-plate-series. = platonic-plate.
platonic-plate-series.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate-series
platonic-plate-series.script-path = ${python-script-folder}/data-set-handler-plate-series.py


# ---------------------------------------------------------------------------
# ---  platonic-microscope  -------------------------------------------------
# ---------------------------------------------------------------------------

# The dropbox for idealized data -- data that doesn't represent real screens, 
# rather data used for testing purposes
platonic-microscope.incoming-dir = ${incoming-root-dir}/incoming-platonic-microscope
platonic-microscope.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
platonic-microscope.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
platonic-microscope.script-path = ${python-script-folder}/data-set-handler-microscope.py
platonic-microscope.staging-dir = ${incoming-root-dir}

platonic-microscope.storage-processor = ch.systemsx.cisd.etlserver.DispatcherStorageProcessor
platonic-microscope.storage-processor.processors = images, analysis
# --- images - accepts all image datasets registrations
platonic-microscope.storage-processor.images = ch.systemsx.cisd.openbis.dss.etl.MicroscopyStorageProcessor
platonic-microscope.storage-processor.images.data-source = imaging-db
# --- analysis - accepts all other datasets (and assumes they are single CSV files)
platonic-microscope.storage-processor.analysis = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
platonic-microscope.storage-processor.analysis.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
platonic-microscope.storage-processor.analysis.data-source = imaging-db
platonic-microscope.storage-processor.analysis.separator = ,
platonic-microscope.storage-processor.analysis.well-name-row = Well
platonic-microscope.storage-processor.analysis.well-name-col = Well
platonic-microscope.storage-processor.analysis.well-name-col-is-alphanum = true

jython-version=2.7