diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracle.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java
similarity index 98%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracle.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java
index 42eb15025923555f2cbcfbbdbbb60a457f4cad54..a5371cc128ec8a5c4247b8b8783f0f31a60eb20d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracle.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
+package ch.systemsx.cisd.openbis.dss.etl;
import java.util.ArrayList;
import java.util.Collections;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java
index 55e57b35e80386e41a11aa4eacfd5eb156ee146b..c99b4206dfde6d5c6fbbbab29db1a59a0e322678 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.openbis.dss.etl.ImageFileExtractorUtils;
+import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
import ch.systemsx.cisd.openbis.dss.etl.UnparsedImageFileInfoLexer;
import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java
index 356ca5a0fc5c11498cb4e746d38ff5dd594512a5..740ae805ffb4bec535dd32a689ca2dd41934b063 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java
@@ -43,6 +43,11 @@ public final class ImageFileInfo
return wellLocationOrNull == null ? null : wellLocationOrNull.getX();
}
+ public Location tryGetWellLocation()
+ {
+ return wellLocationOrNull;
+ }
+
public boolean hasWellLocation()
{
return wellLocationOrNull != null;
@@ -123,8 +128,8 @@ public final class ImageFileInfo
{
return "ImageFileInfo [well=" + wellLocationOrNull + ", tile=" + tileLocation
+ ", channel=" + channelCode + ", path=" + imageRelativePath + ", timepoint="
- + timepointOrNull + ", depth=" + depthOrNull + ", seriesNumber=" + seriesNumberOrNull
- + "]";
+ + timepointOrNull + ", depth=" + depthOrNull + ", seriesNumber="
+ + seriesNumberOrNull + "]";
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index cafe13cc88aeb9cfcb866b1daab91b23607d2f8a..089757a26ac018099b94dc69208e7c6964ec9e49 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -2,11 +2,15 @@ package ch.systemsx.cisd.openbis.dss.etl.jython;
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Properties;
import org.python.util.PythonInterpreter;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
@@ -14,15 +18,19 @@ import ch.systemsx.cisd.etlserver.registrator.IDataSetRegistrationDetailsFactory
import ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.BasicDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
@@ -104,6 +112,44 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
return transaction.commit();
}
+ /**
+ * @return a constant which can be used as a vocabulary term value for $PLATE_GEOMETRY
+ * property of a plate/
+ * @throws UserFailureException if all available geometries in openBIS are too small (there
+ * is a well outside).
+ */
+ public String figureGeometry(
+ DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails)
+ {
+ List<Location> locations =
+ extractLocations(registrationDetails.getDataSetInformation().getImages());
+ List<String> plateGeometries =
+ loadPlateGeometries(registratorState.getGlobalState().getOpenBisService());
+ return PlateGeometryOracle.figureGeometry(locations, plateGeometries);
+ }
+
+ private static List<String> loadPlateGeometries(IEncapsulatedOpenBISService openbisService)
+ {
+ Collection<VocabularyTerm> terms =
+ openbisService.listVocabularyTerms(ScreeningConstants.PLATE_GEOMETRY);
+ List<String> plateGeometries = new ArrayList<String>();
+ for (VocabularyTerm v : terms)
+ {
+ plateGeometries.add(v.getCode());
+ }
+ return plateGeometries;
+ }
+
+ private static List<Location> extractLocations(List<ImageFileInfo> images)
+ {
+ List<Location> locations = new ArrayList<Location>();
+ for (ImageFileInfo image : images)
+ {
+ locations.add(image.tryGetWellLocation());
+ }
+ return locations;
+ }
+
// ----
public IFeaturesBuilder createFeaturesBuilder()
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracleTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracleTest.java
similarity index 98%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracleTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracleTest.java
index 59bf015a32d5bc01c21a930ad423aa32eb8e314c..d92ddc207a2de46eb67aa4c9c0b137eac307e87c 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracleTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracleTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
+package ch.systemsx.cisd.openbis.dss.etl;
import java.util.Arrays;
@@ -23,6 +23,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
/**
* Test cases from {@link PlateGeometryOracle}.