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Commit 67be851f authored by Adam Laskowski's avatar Adam Laskowski
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ssdm-13365: renamed 'test-data' to 'test-miscellaneous'

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1 merge request!40SSDM-13578 : 2PT : Database and V3 Implementation - include the new AFS "free"...
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test-data/.pydevproject → test-miscellaneous/.pydevproject
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test-data/screening/config/dss-service.properties → test-miscellaneous/screening/config/dss-service.properties
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# Unique code of this Data Store Server. Not more than 40 characters. # Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = dss-screening-platonic data-store-server-code=dss-screening-platonic
# host name of the machine on which the datastore server is running # host name of the machine on which the datastore server is running
host-address = http://localhost host-address=http://localhost
# parent directory of the store directory and all the dropboxes # parent directory of the store directory and all the dropboxes
root-dir = targets/platonic root-dir=targets/platonic
# The root directory of the data store # The root directory of the data store
storeroot-dir = ${root-dir}/store storeroot-dir=${root-dir}/store
# The directory for the python scripts (and other configuration data) # The directory for the python scripts (and other configuration data)
python-script-folder = ../test-data/screening/etc python-script-folder=../test-miscellaneous/screening/etc
# The directory where the command queue file is located; defaults to storeroot-dir
# The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir=
commandqueue-dir =
# Create any incoming directories that do not already exist # Create any incoming directories that do not already exist
incoming-dir-create = true incoming-dir-create=true
# Port # Port
port = 8889 port=8889
use-ssl = false use-ssl=false
# Session timeout in minutes # Session timeout in minutes
session-timeout = 30 session-timeout=30
# Path to the keystore # Path to the keystore
keystore.path = dist/etc/openBIS.keystore keystore.path=dist/etc/openBIS.keystore
# Password of the keystore # Password of the keystore
keystore.password = changeit keystore.password=changeit
# Key password of the keystore # Key password of the keystore
keystore.key-password = changeit keystore.key-password=changeit
# The check interval (in seconds) # The check interval (in seconds)
check-interval = 5 check-interval=5
# The time-out for clean up work in the shutdown sequence (in seconds). # 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 # Note that that the maximal time for the shutdown sequence to complete can be as large
# as twice this time. # as twice this time.
# Remark: On a network file system, it is not recommended to turn this value to something # Remark: On a network file system, it is not recommended to turn this value to something
# lower than 180. # lower than 180.
shutdown-timeout = 2 shutdown-timeout=2
# If free disk space goes below value defined here, a notification email will be sent. # 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 # 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. # specified or if value is negative, the system will not be watching.
highwater-mark = 1000 highwater-mark=1000
# If a data set is successfully registered it sends out an email to the registrator.
# 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 # 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. # does not affect the mails which are sent, when the data set could not be registered.
notify-successful-registration = false notify-successful-registration=false
# The URL of the openBIS server # The URL of the openBIS server
server-url = ${host-address}:8888 server-url=${host-address}:8888
# The username to use when contacting the openBIS server # The username to use when contacting the openBIS server
username = etlserver username=etlserver
# The password for the etlserver user who contacts the openBIS server # The password for the etlserver user who contacts the openBIS server
password = etlserver_password password=etlserver_password
# The base URL for Web client access to the data store server. # The base URL for Web client access to the data store server.
download-url = ${host-address}:8889 download-url=${host-address}:8889
# SMTP properties (must start with 'mail' to be considered). # SMTP properties (must start with 'mail' to be considered).
# The current configuration saves the emails in the file system in the root directory # The current configuration saves the emails in the file system in the root directory
mail.smtp.host = file://${root-dir}/emails mail.smtp.host=file://${root-dir}/emails
# mail.smtp.host = localhost # mail.smtp.host = localhost
# mail.from = datastore_server@ethz.ch # mail.from = datastore_server@ethz.ch
# mail.smtp.user = # mail.smtp.user =
# mail.smtp.password = # mail.smtp.password =
core-plugins-folder=../screening/source/core-plugins
core-plugins-folder = ../screening/source/core-plugins enabled-technologies=screening
enabled-technologies = screening imaging-database.kind=platonic
screening-sql-root-folder=source/
imaging-database.kind = platonic
screening-sql-root-folder = source/
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# (optional) archiver configuration # (optional) archiver configuration
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# Configuration of an archiver task. All properties are prefixed with 'archiver.'. # 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 specification (together with the list of packages this class belongs to).
#archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver #archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# INTERNAL CONFIGURATION, # INTERNAL CONFIGURATION,
# Do not change this part unless you are developing openBIS extensions. # Do not change this part unless you are developing openBIS extensions.
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# screening database specification # screening database specification
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
data-sources=path-info-db
data-sources = path-info-db
# Data source for pathinfo database # Data source for pathinfo database
path-info-db.version-holder-class = ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder path-info-db.version-holder-class=ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
path-info-db.databaseEngineCode = postgresql path-info-db.databaseEngineCode=postgresql
path-info-db.basicDatabaseName = pathinfo path-info-db.basicDatabaseName=pathinfo
path-info-db.databaseKind = platonic path-info-db.databaseKind=platonic
path-info-db.scriptFolder = ../datastore_server/source/sql path-info-db.scriptFolder=../datastore_server/source/sql
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# reporting and processing plugins configuration # reporting and processing plugins configuration
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name. # Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
reporting-plugins = well-image-analysis-graph, csv-viewer reporting-plugins=well-image-analysis-graph, csv-viewer
well-image-analysis-graph.label=Image Analysis Graphs
well-image-analysis-graph.label = Image Analysis Graphs well-image-analysis-graph.dataset-types=HCS_ANALYSIS_WELL_FEATURES
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.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisGraphReportingPlugin well-image-analysis-graph.servlet-path=analysis_graph/
well-image-analysis-graph.servlet-path = analysis_graph/ well-image-analysis-graph.properties-file=${python-script-folder}/analysis-graph.properties
well-image-analysis-graph.properties-file = ${python-script-folder}/analysis-graph.properties well-image-analysis-graph.servlet.class=ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet
well-image-analysis-graph.servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet well-image-analysis-graph.servlet.path=/${well-image-analysis-graph.servlet-path}*
well-image-analysis-graph.servlet.path = /${well-image-analysis-graph.servlet-path}* well-image-analysis-graph.servlet.properties-file=${well-image-analysis-graph.properties-file}
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.label = CSV View csv-viewer.class=ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
csv-viewer.dataset-types = HCS_IMAGE_ANALYSIS_DATA csv-viewer.separator=,
csv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
csv-viewer.separator = ,
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
maintenance-plugins=path-info-deletion, post-registration
maintenance-plugins = path-info-deletion, post-registration path-info-feeding.class=ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
path-info-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask path-info-feeding.execute-only-once=true
path-info-feeding.execute-only-once = true
# Maintenance task for deleting entries in pathinfo database after deletion of data sets # 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.class=ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
path-info-deletion.interval = 120 path-info-deletion.interval=120
path-info-deletion.data-source = path-info-db path-info-deletion.data-source=path-info-db
path-info-deletion.data-set-perm-id = CODE path-info-deletion.data-set-perm-id=CODE
path-info-deletion.data-set-table-name = data_sets 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
# 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.class = ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask post-registration.interval=30
post-registration.interval = 30 post-registration.cleanup-tasks-folder=targets/cleanup-tasks
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. # 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. # 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.ignore-data-sets-before-date = 2011-04-18
post-registration.last-seen-data-set-file = targets/last-seen-data-set post-registration.last-seen-data-set-file=targets/last-seen-data-set
post-registration.post-registration-tasks = pathinfo-feeding post-registration.post-registration-tasks=pathinfo-feeding
post-registration.pathinfo-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask post-registration.pathinfo-feeding.class=ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# DROPBOXES CONFIGURATION # DROPBOXES CONFIGURATION
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
incoming-root-dir=${root-dir}
incoming-root-dir = ${root-dir} # Globally used separator character which separates entities in a data set file name
data-set-file-name-entity-separator=_
# Globally used separator character which separates entities in a data set file name # The period of no write access that needs to pass before an incoming data item is considered
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]. # 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. # Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
quiet-period=10 quiet-period=10
# code of the default space in openBIS to which the data will be imported # code of the default space in openBIS to which the data will be imported
import-space-code = PLATONIC import-space-code=PLATONIC
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # 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' # 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 inputs=platonic-plate, platonic-plate-splitted, platonic-plate-overlay, platonic-plate-features, platonic-plate-series, platonic-microscope
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# --- platonic-plate ------------------------------------------------------ # --- platonic-plate ------------------------------------------------------
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# The dropbox for idealized data -- data that doesn't represent real screens,
# The dropbox for idealized data -- data that doesn't represent real screens,
# rather data used for testing purposes # rather data used for testing purposes
platonic-plate.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate platonic-plate.incoming-dir=${incoming-root-dir}/incoming-platonic-plate
platonic-plate.incoming-data-completeness-condition = auto-detection platonic-plate.incoming-data-completeness-condition=auto-detection
# The extractor class to use for code extraction # 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.top-level-data-set-handler=ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
platonic-plate.script-path = ${python-script-folder}/data-set-handler-plate.py platonic-plate.script-path=${python-script-folder}/data-set-handler-plate.py
platonic-plate.staging-dir = ${incoming-root-dir} platonic-plate.staging-dir=${incoming-root-dir}
platonic-plate.storage-processor=ch.systemsx.cisd.etlserver.DispatcherStorageProcessor
platonic-plate.storage-processor = ch.systemsx.cisd.etlserver.DispatcherStorageProcessor platonic-plate.storage-processor.processors=images, analysis
platonic-plate.storage-processor.processors = images, analysis
# --- images - accepts all image datasets registrations # --- images - accepts all image datasets registrations
platonic-plate.storage-processor.images = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor platonic-plate.storage-processor.images=ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
platonic-plate.storage-processor.images.data-source = imaging-db platonic-plate.storage-processor.images.data-source=imaging-db
# --- analysis - accepts all other datasets (and assumes they are single CSV files) # --- 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=ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
platonic-plate.storage-processor.analysis.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor 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.data-source=imaging-db
platonic-plate.storage-processor.analysis.separator = , platonic-plate.storage-processor.analysis.separator=,
platonic-plate.storage-processor.analysis.well-name-row = Well 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=Well
platonic-plate.storage-processor.analysis.well-name-col-is-alphanum = true platonic-plate.storage-processor.analysis.well-name-col-is-alphanum=true
platonic-plate-splitted.=platonic-plate.
platonic-plate-splitted. = platonic-plate. platonic-plate-splitted.incoming-dir=${incoming-root-dir}/incoming-platonic-plate-splitted
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-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. = platonic-plate. platonic-plate-overlay.script-path=${python-script-folder}/data-set-handler-plate-overlays.py
platonic-plate-overlay.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate-overlays platonic-plate-features.=platonic-plate.
platonic-plate-overlay.script-path = ${python-script-folder}/data-set-handler-plate-overlays.py platonic-plate-features.incoming-dir=${incoming-root-dir}/incoming-platonic-plate-features
platonic-plate-features.script-path=${python-script-folder}/data-set-handler-plate-features.py
platonic-plate-features. = platonic-plate. platonic-plate-series.=platonic-plate.
platonic-plate-features.incoming-dir = ${incoming-root-dir}/incoming-platonic-plate-features platonic-plate-series.incoming-dir=${incoming-root-dir}/incoming-platonic-plate-series
platonic-plate-features.script-path = ${python-script-folder}/data-set-handler-plate-features.py platonic-plate-series.script-path=${python-script-folder}/data-set-handler-plate-series.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 ------------------------------------------------- # --- platonic-microscope -------------------------------------------------
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# The dropbox for idealized data -- data that doesn't represent real screens,
# The dropbox for idealized data -- data that doesn't represent real screens,
# rather data used for testing purposes # rather data used for testing purposes
platonic-microscope.incoming-dir = ${incoming-root-dir}/incoming-platonic-microscope platonic-microscope.incoming-dir=${incoming-root-dir}/incoming-platonic-microscope
platonic-microscope.incoming-data-completeness-condition = auto-detection platonic-microscope.incoming-data-completeness-condition=auto-detection
# The extractor class to use for code extraction # 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.top-level-data-set-handler=ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
platonic-microscope.script-path = ${python-script-folder}/data-set-handler-microscope.py platonic-microscope.script-path=${python-script-folder}/data-set-handler-microscope.py
platonic-microscope.staging-dir = ${incoming-root-dir} platonic-microscope.staging-dir=${incoming-root-dir}
platonic-microscope.storage-processor=ch.systemsx.cisd.etlserver.DispatcherStorageProcessor
platonic-microscope.storage-processor = ch.systemsx.cisd.etlserver.DispatcherStorageProcessor platonic-microscope.storage-processor.processors=images, analysis
platonic-microscope.storage-processor.processors = images, analysis
# --- images - accepts all image datasets registrations # --- images - accepts all image datasets registrations
platonic-microscope.storage-processor.images = ch.systemsx.cisd.openbis.dss.etl.MicroscopyStorageProcessor platonic-microscope.storage-processor.images=ch.systemsx.cisd.openbis.dss.etl.MicroscopyStorageProcessor
platonic-microscope.storage-processor.images.data-source = imaging-db platonic-microscope.storage-processor.images.data-source=imaging-db
# --- analysis - accepts all other datasets (and assumes they are single CSV files) # --- 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=ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
platonic-microscope.storage-processor.analysis.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor 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.data-source=imaging-db
platonic-microscope.storage-processor.analysis.separator = , platonic-microscope.storage-processor.analysis.separator=,
platonic-microscope.storage-processor.analysis.well-name-row = Well 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=Well
platonic-microscope.storage-processor.analysis.well-name-col-is-alphanum = true platonic-microscope.storage-processor.analysis.well-name-col-is-alphanum=true
jython-version=2.7 jython-version=2.7
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