From 6a779227f31bcd387cd862b1e41a8520e5a88b03 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Wed, 11 May 2011 07:33:51 +0000
Subject: [PATCH] use service.properties from template for test-screening
SVN: 21223
---
.../etc/service.properties | 74 +++++++++++++++++--
.../genedata-dropboxes-service.properties | 63 ----------------
.../integration-tests-service.properties | 19 -----
integration-tests/test-screening.sh | 5 +-
4 files changed, 71 insertions(+), 90 deletions(-)
delete mode 100644 integration-tests/templates/datastore_server_screening/genedata-dropboxes-service.properties
delete mode 100644 integration-tests/templates/datastore_server_screening/integration-tests-service.properties
diff --git a/integration-tests/templates/datastore_server_screening/etc/service.properties b/integration-tests/templates/datastore_server_screening/etc/service.properties
index be3a27e0466..74d5858fc10 100644
--- a/integration-tests/templates/datastore_server_screening/etc/service.properties
+++ b/integration-tests/templates/datastore_server_screening/etc/service.properties
@@ -28,7 +28,7 @@ keystore.password = changeit
keystore.key-password = changeit
# The check interval (in seconds)
-check-interval = 60
+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
@@ -85,11 +85,11 @@ mail.smtp.host = file://${root-dir}
# 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.databaseEngineCode = postgresql
imaging-db.basicDatabaseName = imaging
-imaging-db.databaseKind = productive
+imaging-db.databaseKind = integration_tests
imaging-db.scriptFolder = sql
imaging-db.owner =
imaging-db.password =
@@ -99,6 +99,14 @@ imaging-db.password =
imaging-db.adminUser =
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
# ---------------------------------------------------------------------------
@@ -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
# 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 = 300
+quiet-period = 5
# code of the default space in openBIS to which the data will be imported
import-space-code = DEMO
# 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=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
#microscopy-series-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyBlackboxSeriesStorageProcessor
#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
diff --git a/integration-tests/templates/datastore_server_screening/genedata-dropboxes-service.properties b/integration-tests/templates/datastore_server_screening/genedata-dropboxes-service.properties
deleted file mode 100644
index cbb8a5e943f..00000000000
--- a/integration-tests/templates/datastore_server_screening/genedata-dropboxes-service.properties
+++ /dev/null
@@ -1,63 +0,0 @@
-
-# ---------------------------------------------------------------------------
-# 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
diff --git a/integration-tests/templates/datastore_server_screening/integration-tests-service.properties b/integration-tests/templates/datastore_server_screening/integration-tests-service.properties
deleted file mode 100644
index a361dd6572a..00000000000
--- a/integration-tests/templates/datastore_server_screening/integration-tests-service.properties
+++ /dev/null
@@ -1,19 +0,0 @@
-
-# ---------------------------------------------------------------------------
-# 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
diff --git a/integration-tests/test-screening.sh b/integration-tests/test-screening.sh
index 206e5266561..25fafce9b69 100755
--- a/integration-tests/test-screening.sh
+++ b/integration-tests/test-screening.sh
@@ -79,9 +79,8 @@ function install_dss_screening {
mv $dss_dest/datastore_server/* $dss_dest
rmdir $dss_dest/datastore_server
- # extend distribution configuration
- cat $dss_template/integration-tests-service.properties >> $dss_dest/etc/service.properties
- cat $dss_template/genedata-dropboxes-service.properties >> $dss_dest/etc/service.properties
+ # override default DSS configuration
+ cp -v $dss_template/etc/service.properties $dss_dest/etc
}
function install_screening_api {
--
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