LMS-1546 HCS integration tests resources: plates, feature vectors, minimal test database

SVN: 16742

integration-tests/templates/datastore_server_screening/genedata-dropboxes-service.properties

+
+# ---------------------------------------------------------------------------
+# These lines override the distribution configuration to make it possible
+# to test Genedata specific dropboxes.
+# ---------------------------------------------------------------------------
+
+inputs=split-channels-images, merged-channels-images, image-analysis-results, genedata-merged-channels-images, genedata-image-analysis-results
+
+# ---------------------------------------------------------------------------
+# GENEDATA formats
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+genedata-merged-channels-images.incoming-dir = ${incoming-root-dir}/incoming-images-genedata
+genedata-merged-channels-images.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+genedata-merged-channels-images.data-set-info-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.DataSetInfoExtractorForDataAcquisition
+# Separator used to extract the barcode in the data set file name
+genedata-merged-channels-images.data-set-info-extractor.entity-separator = .
+genedata-merged-channels-images.data-set-info-extractor.index-of-sample-code = 0
+genedata-merged-channels-images.data-set-info-extractor.index-of-data-producer-code = 
+genedata-merged-channels-images.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+genedata-merged-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+genedata-merged-channels-images.type-extractor.file-format-type = JPG
+genedata-merged-channels-images.type-extractor.locator-type = RELATIVE_LOCATION
+genedata-merged-channels-images.type-extractor.data-set-type = HCS_IMAGE
+genedata-merged-channels-images.type-extractor.is-measured = true
+
+genedata-merged-channels-images.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+genedata-merged-channels-images.storage-processor.well_geometry = 1x1
+genedata-merged-channels-images.storage-processor.channel-names = DAPI, GFP
+# Available values: RED, BLUE or GREEN
+genedata-merged-channels-images.storage-processor.extract-single-image-channels = BLUE, GREEN
+genedata-merged-channels-images.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.HCSImageFileExtractor
+genedata-merged-channels-images.storage-processor.data-source = imaging-db
+
+#  --------------------------------------------------------------
+
+# The directory to watch for incoming data.
+genedata-image-analysis-results.incoming-dir = ${incoming-root-dir}/incoming-analysis-genedata
+genedata-image-analysis-results.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+genedata-image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.DataSetInfoExtractorForImageAnalysis
+# Separator used to extract the barcode in the data set file name
+genedata-image-analysis-results.data-set-info-extractor.entity-separator = .
+genedata-image-analysis-results.data-set-info-extractor.index-of-sample-code = 0
+genedata-image-analysis-results.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+genedata-image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+genedata-image-analysis-results.type-extractor.file-format-type = CSV
+genedata-image-analysis-results.type-extractor.locator-type = RELATIVE_LOCATION
+genedata-image-analysis-results.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA
+genedata-image-analysis-results.type-extractor.is-measured = false
+
+# The storage processor (IStorageProcessor implementation)
+genedata-image-analysis-results.storage-processor = ch.systemsx.cisd.openbis.dss.etl.genedata.FeatureStorageProcessor
+genedata-image-analysis-results.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+genedata-image-analysis-results.storage-processor.data-source = imaging-db
\ No newline at end of file

integration-tests/templates/datastore_server_screening/integration-tests-service.properties

+
+# ---------------------------------------------------------------------------
+# These lines override the distribution configuration to make it possible
+# to run integration tests.
+# ---------------------------------------------------------------------------
+ 
+check-interval = 5
+quiet-period = 5

integration-tests/templates/datastore_server_screening/local-tests-service.properties

+
+# ---------------------------------------------------------------------------
+# These lines override the distribution configuration to make it possible
+# to run integration tests locally from Eclipse.
+# ---------------------------------------------------------------------------
+ 
+root-dir = targets
+incoming-root-dir = ${root-dir}
+keystore.path = dist/etc/openBIS.keystore
+
+server-url = http://localhost:8888
+download-url = http://localhost:8889
+use-ssl = false
+
+imaging-db.scriptFolder = source/sql

integration-tests/templates/openBIS-server-screening/openbis.conf

+#
+# openBIS configuration file
+#
+
+#
+# Home directory of the JRE that should be used
+#
+#JAVA_HOME=${JAVA_HOME:=/usr/java/latest}
+
+#
+# General options to the JRE
+#
+JAVA_OPTS=${JAVA_OPTS:=-server -Djavax.net.ssl.trustStore=etc/openBIS.keystore}
+
+#
+# Memory options to the JRE
+#
+JAVA_MEM_OPTS="-Xmx512m -Xms512m -XX:MaxPermSize=256m"