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Commit 6a779227 authored by kaloyane's avatar kaloyane
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use service.properties from template for test-screening 

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integration-tests/templates/datastore_server_screening/etc/service.properties
+ 69
− 5
View file @ 6a779227
...@@ -28,7 +28,7 @@ keystore.password = changeit ...@@ -28,7 +28,7 @@ keystore.password = changeit
keystore.key-password = changeit keystore.key-password = changeit
# The check interval (in seconds) # The check interval (in seconds)
check-interval = 60 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
...@@ -85,11 +85,11 @@ mail.smtp.host = file://${root-dir} ...@@ -85,11 +85,11 @@ mail.smtp.host = file://${root-dir}
# screening database specification # screening database specification
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
data-sources = imaging-db data-sources = path-info-db, imaging-db
imaging-db.version-holder-class = ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseVersionHolder imaging-db.version-holder-class = ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseVersionHolder
imaging-db.databaseEngineCode = postgresql imaging-db.databaseEngineCode = postgresql
imaging-db.basicDatabaseName = imaging imaging-db.basicDatabaseName = imaging
imaging-db.databaseKind = productive imaging-db.databaseKind = integration_tests
imaging-db.scriptFolder = sql imaging-db.scriptFolder = sql
imaging-db.owner = imaging-db.owner =
imaging-db.password = imaging-db.password =
...@@ -99,6 +99,14 @@ imaging-db.password = ...@@ -99,6 +99,14 @@ imaging-db.password =
imaging-db.adminUser = imaging-db.adminUser =
imaging-db.adminPassword = imaging-db.adminPassword =
# 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 = screening_integration_tests
path-info-db.scriptFolder = sql
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# reporting and processing plugins configuration # reporting and processing plugins configuration
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
...@@ -184,14 +192,14 @@ data-set-file-name-entity-separator = _ ...@@ -184,14 +192,14 @@ data-set-file-name-entity-separator = _
# The period of no write access that needs to pass before an incoming data item is considered # 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 = 300 quiet-period = 5
# 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 = DEMO import-space-code = DEMO
# 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=merged-channels-images, split-channels-images, image-analysis-results inputs=split-channels-images, merged-channels-images, image-analysis-results, genedata-merged-channels-images, genedata-image-analysis-results
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
...@@ -374,3 +382,59 @@ image-analysis-results.storage-processor.well-name-col-is-alphanum = true ...@@ -374,3 +382,59 @@ image-analysis-results.storage-processor.well-name-col-is-alphanum = true
#microscopy-series-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyBlackboxSeriesStorageProcessor #microscopy-series-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyBlackboxSeriesStorageProcessor
#microscopy-series-dropbox.storage-processor.data-source = imaging-db #microscopy-series-dropbox.storage-processor.data-source = imaging-db
# ---------------------------------------------------------------------------
# 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
integration-tests/templates/datastore_server_screening/genedata-dropboxes-service.properties deleted 100644 → 0
+ 0
− 63
View file @ 6681c2ac
# ---------------------------------------------------------------------------
# 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 deleted 100644 → 0
+ 0
− 19
View file @ 6681c2ac
# ---------------------------------------------------------------------------
# These lines override the distribution configuration to make it possible
# to run integration tests.
# ---------------------------------------------------------------------------
check-interval = 5
quiet-period = 5
imaging-db.databaseKind = integration_tests
data-sources = path-info-db, imaging-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 = screening_integration_tests
path-info-db.scriptFolder = sql
integration-tests/test-screening.sh
+ 2
− 3
View file @ 6a779227
...@@ -79,9 +79,8 @@ function install_dss_screening { ...@@ -79,9 +79,8 @@ function install_dss_screening {
mv $dss_dest/datastore_server/* $dss_dest mv $dss_dest/datastore_server/* $dss_dest
rmdir $dss_dest/datastore_server rmdir $dss_dest/datastore_server
# extend distribution configuration # override default DSS configuration
cat $dss_template/integration-tests-service.properties >> $dss_dest/etc/service.properties cp -v $dss_template/etc/service.properties $dss_dest/etc
cat $dss_template/genedata-dropboxes-service.properties >> $dss_dest/etc/service.properties
} }
function install_screening_api { function install_screening_api {
......
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