From 79436a0c6188e732cb76e19830c86e0695d13afb Mon Sep 17 00:00:00 2001
From: izabel <izabel>
Date: Wed, 8 Sep 2010 07:53:26 +0000
Subject: [PATCH] [LMS-1715] small refactoring; unit tests
SVN: 17753
---
.../biozentrum/BZDataSetInfoExtractor.java | 173 ++++--------------
.../BZDatasetDirectoryNameTokenizer.java | 65 +++++++
.../etl/biozentrum/HCSImageFileExtractor.java | 22 +--
.../etl/biozentrum/PlateGeometryOracle.java | 6 +-
.../openbis/dss/etl/biozentrum/Utils.java | 143 +++++++++++++++
.../biozentrum/PlateGeometryOracleTest.java | 152 +++++++++++++++
...eFileExtractorTest.java => UtilsTest.java} | 9 +-
7 files changed, 411 insertions(+), 159 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/Utils.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracleTest.java
rename screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/{HCSImageFileExtractorTest.java => UtilsTest.java} (81%)
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 74e5b065849..404ad8a7e60 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
@@ -23,28 +23,17 @@ import java.util.List;
import java.util.Properties;
import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
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.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTermValueEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
@@ -52,7 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
- * Data set info extractor dealing with BZ data. Creates experiments and plates if needed.
+ * Data set info extractor dealing with iBrain data. Creates experiments and plates if needed.
*
* @author Izabela Adamczyk
*/
@@ -63,23 +52,24 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
static final String PROJECT_CODE = "project-code";
- private final Properties properties;
+ private final String spaceCode;
+
+ private final String projectCode;
public BZDataSetInfoExtractor(final Properties properties)
{
- this.properties = properties;
+ spaceCode = PropertyUtils.getMandatoryProperty(properties, SPACE_CODE);
+ projectCode = PropertyUtils.getMandatoryProperty(properties, PROJECT_CODE);
}
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
{
- final DataSetInformation dataSetInformation = new DataSetInformation();
- DirectoryDatasetInfoExtractor tokens =
- new DirectoryDatasetInfoExtractor(FilenameUtils.getBaseName(incomingDataSetPath
+
+ BZDatasetDirectoryNameTokenizer tokens =
+ new BZDatasetDirectoryNameTokenizer(FilenameUtils.getBaseName(incomingDataSetPath
.getPath()));
- String spaceCode = PropertyUtils.getMandatoryProperty(properties, SPACE_CODE);
- String projectCode = PropertyUtils.getMandatoryProperty(properties, PROJECT_CODE);
String sampleCode = getSampleCode(tokens);
String experimentCode = getExperiment(tokens);
ExperimentIdentifier experimentIdentifier =
@@ -87,26 +77,12 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
SampleIdentifier sampleIdentifier =
new SampleIdentifier(new GroupIdentifier(DatabaseInstanceIdentifier.createHome(),
spaceCode), sampleCode);
+
Sample sampleOrNull = openbisService.tryGetSampleWithExperiment(sampleIdentifier);
if (sampleOrNull == null)
{
- Collection<VocabularyTerm> terms =
- openbisService.listVocabularyTerms(ScreeningConstants.PLATE_GEOMETRY);
- List<String> plateGeometries = new ArrayList<String>();
- for (VocabularyTerm v : terms)
- {
- plateGeometries.add(v.getCode());
- }
- List<File> imageFiles = ImageFileExtractorUtils.listImageFiles(incomingDataSetPath);
- List<Location> plateLocations = new ArrayList<Location>();
- for (File imageFile : imageFiles)
- {
- String baseName = FilenameUtils.getBaseName(imageFile.getPath());
- String plateLocationToken =
- HCSImageFileExtractor.extractFileInfo(baseName).getPlateLocationToken();
- plateLocations.add(Location
- .tryCreateLocationFromTransposedMatrixCoordinate(plateLocationToken));
- }
+ List<String> plateGeometries = loadPlateGeometries(openbisService);
+ List<Location> plateLocations = Utils.extractPlateLocations(incomingDataSetPath);
String plateGeometry =
PlateGeometryOracle.figureGeometry(plateLocations, plateGeometries);
registerSampleWithExperiment(openbisService, sampleIdentifier, experimentIdentifier,
@@ -118,6 +94,17 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
sampleIdentifier));
}
}
+ checkSampleExperiment(experimentIdentifier, sampleIdentifier, sampleOrNull);
+
+ final DataSetInformation dataSetInformation = new DataSetInformation();
+ dataSetInformation.setSpaceCode(spaceCode);
+ dataSetInformation.setSampleCode(sampleCode);
+ return dataSetInformation;
+ }
+
+ private void checkSampleExperiment(ExperimentIdentifier experimentIdentifier,
+ SampleIdentifier sampleIdentifier, Sample sampleOrNull)
+ {
if (sampleOrNull.getExperiment() == null
|| new ExperimentIdentifier(sampleOrNull.getExperiment())
.equals(experimentIdentifier) == false)
@@ -126,9 +113,18 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
"Sample '%s' is not part of experiment '%s'", sampleIdentifier,
experimentIdentifier));
}
- dataSetInformation.setSpaceCode(spaceCode);
- dataSetInformation.setSampleCode(sampleCode);
- return dataSetInformation;
+ }
+
+ private 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 void registerSampleWithExperiment(IEncapsulatedOpenBISService openbisService,
@@ -138,7 +134,7 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
Experiment experimentOrNull = openbisService.tryToGetExperiment(experimentIdentifier);
if (experimentOrNull == null)
{
- registerExperiment(openbisService, experimentIdentifier);
+ openbisService.registerExperiment(Utils.createExperimentSIRNAHCS(experimentIdentifier));
experimentOrNull = openbisService.tryToGetExperiment(experimentIdentifier);
if (experimentOrNull == null)
{
@@ -146,107 +142,18 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
experimentIdentifier));
}
}
- NewSample sample = new NewSample();
- sample.setExperimentIdentifier(experimentIdentifier.toString());
- sample.setIdentifier(sampleIdentifier.toString());
- SampleType sampleType = new SampleType();
- sampleType.setCode(ScreeningConstants.PLATE_PLUGIN_TYPE_CODE);
- sample.setSampleType(sampleType);
- sample.setProperties(createPlateGeometryProperty(plateGeometry));
- openbisService.registerSample(sample, null);
+ openbisService.registerSample(Utils.createPlate(sampleIdentifier, experimentIdentifier,
+ plateGeometry), null);
}
- private static IEntityProperty[] createPlateGeometryProperty(String plateGeometry)
- {
- List<IEntityProperty> sampleProperties = new ArrayList<IEntityProperty>();
- VocabularyTermValueEntityProperty property = new VocabularyTermValueEntityProperty();
- VocabularyTerm vocabularyTerm = new VocabularyTerm();
- vocabularyTerm.setCode(plateGeometry);
- property.setVocabularyTerm(vocabularyTerm);
- PropertyType propertyType = new PropertyType();
- DataType dataType = new DataType();
- dataType.setCode(DataTypeCode.CONTROLLEDVOCABULARY);
- propertyType.setDataType(dataType);
- propertyType.setCode(ScreeningConstants.PLATE_GEOMETRY);
- property.setPropertyType(propertyType);
- sampleProperties.add(property);
- return sampleProperties.toArray(new IEntityProperty[sampleProperties.size()]);
- }
-
- private static IEntityProperty[] createDescriptionProperty(String description)
- {
- List<IEntityProperty> properties = new ArrayList<IEntityProperty>();
- GenericValueEntityProperty property = new GenericValueEntityProperty();
- property.setValue(description);
- PropertyType propertyType = new PropertyType();
- DataType dataType = new DataType();
- dataType.setCode(DataTypeCode.VARCHAR);
- propertyType.setDataType(dataType);
- propertyType.setCode(ScreeningConstants.DESCRIPTION);
- property.setPropertyType(propertyType);
- properties.add(property);
- return properties.toArray(new IEntityProperty[properties.size()]);
- }
-
- private static void registerExperiment(IEncapsulatedOpenBISService openbisService,
- ExperimentIdentifier experimentIdentifier)
- {
- NewExperiment experiment = new NewExperiment();
- experiment.setExperimentTypeCode(ScreeningConstants.SIRNA_HCS);
- experiment.setIdentifier(experimentIdentifier.toString());
- experiment.setProperties(createDescriptionProperty("-"));
- openbisService.registerExperiment(experiment);
- }
-
- private String getExperiment(DirectoryDatasetInfoExtractor tokens)
+ private static String getExperiment(BZDatasetDirectoryNameTokenizer tokens)
{
return tokens.getExperimentToken();
}
- private String getSampleCode(DirectoryDatasetInfoExtractor tokens)
+ private static String getSampleCode(BZDatasetDirectoryNameTokenizer tokens)
{
return "P_" + tokens.getExperimentToken() + "_" + tokens.getTimestampToken();
}
- private class DirectoryDatasetInfoExtractor
- {
- private final String experimentToken;
-
- private final String plateToken;
-
- private final String barcodeToken;
-
- private final String timestampToken;
-
- DirectoryDatasetInfoExtractor(String identifier)
- {
- String[] namedParts = StringUtils.split(identifier, "_");
- experimentToken = StringUtils.split(namedParts[0], "-")[1];
- plateToken = StringUtils.split(namedParts[1], "-")[1];
- barcodeToken = StringUtils.split(namedParts[2], "-")[1];
- timestampToken = StringUtils.split(namedParts[3], "-")[1];
- }
-
- public String getExperimentToken()
- {
- return experimentToken;
- }
-
- public String getPlateToken()
- {
- return plateToken;
- }
-
- public String getBarcodeToken()
- {
- return barcodeToken;
- }
-
- public String getTimestampToken()
- {
- return timestampToken;
- }
-
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java
new file mode 100644
index 00000000000..30e90f38f78
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java
@@ -0,0 +1,65 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * Extracts useful information from dataset directory name specific to iBrain2.
+ *
+ * @author Izabela Adamczyk
+ */
+public class BZDatasetDirectoryNameTokenizer
+{
+ private final String experimentToken;
+
+ private final String plateToken;
+
+ private final String barcodeToken;
+
+ private final String timestampToken;
+
+ BZDatasetDirectoryNameTokenizer(String identifier)
+ {
+ String[] namedParts = StringUtils.split(identifier, "_");
+ experimentToken = StringUtils.split(namedParts[0], "-")[1];
+ plateToken = StringUtils.split(namedParts[1], "-")[1];
+ barcodeToken = StringUtils.split(namedParts[2], "-")[1];
+ timestampToken = StringUtils.split(namedParts[3], "-")[1];
+ }
+
+ public String getExperimentToken()
+ {
+ return experimentToken;
+ }
+
+ public String getPlateToken()
+ {
+ return plateToken;
+ }
+
+ public String getBarcodeToken()
+ {
+ return barcodeToken;
+ }
+
+ public String getTimestampToken()
+ {
+ return timestampToken;
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractor.java
index 27ec8b57480..53b72a38e00 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractor.java
@@ -19,13 +19,10 @@ package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
import java.io.File;
import java.util.Properties;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang.StringUtils;
-
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
- * A <code>IHCSImageFileExtractor</code> implementation suitable for <i>BioZentrum</i>.
+ * A <code>IHCSImageFileExtractor</code> implementation suitable for <i>iBrain</i>.
*
* @author Izabela Adamczyk
*/
@@ -40,22 +37,7 @@ public class HCSImageFileExtractor extends ch.systemsx.cisd.openbis.dss.etl.HCSI
@Override
protected final ImageFileInfo tryExtractImageInfo(File imageFile, SampleIdentifier datasetSample)
{
- return extractFileInfo(FilenameUtils.getBaseName(imageFile.getPath()));
- }
-
- static ImageFileInfo extractFileInfo(String text)
- {
- String[] namedParts = StringUtils.split(text, "_");
- final String plateLocationToken = StringUtils.split(namedParts[3], "-")[1];
- final String wellLocationToken = StringUtils.split(namedParts[4], "-")[1];
- final String timepointToken = StringUtils.split(namedParts[5], "-")[1];
- final String channelToken = StringUtils.split(namedParts[6], "-")[1];
- ImageFileInfo info = new ImageFileInfo();
- info.setPlateLocationToken(plateLocationToken);
- info.setWellLocationToken(wellLocationToken);
- info.setChannelToken(channelToken);
- info.setTimepointToken(timepointToken);
- return info;
+ return Utils.extractImageFileInfo(imageFile);
}
}
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/biozentrum/PlateGeometryOracle.java
index 3af0c0fbf01..42eb1502592 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracle.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracle.java
@@ -92,6 +92,10 @@ public class PlateGeometryOracle
static private boolean isEnough(Geometry geometry, Location location)
{
- return geometry.getDimX() >= location.getX() && geometry.getDimY() >= location.getY();
+ int dimX = geometry.getDimX();
+ int x = location.getX();
+ int dimY = geometry.getDimY();
+ int y = location.getY();
+ return dimX >= x && dimY >= y;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/Utils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/Utils.java
new file mode 100644
index 00000000000..e9438319414
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/Utils.java
@@ -0,0 +1,143 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.dss.etl.ImageFileExtractorUtils;
+import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor.ImageFileInfo;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTermValueEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Utility class containing methods useful in iBrain integration.
+ *
+ * @author Izabela Adamczyk
+ */
+public class Utils
+{
+ static ImageFileInfo extractImageFileInfo(File imageFile)
+ {
+ return extractBZImageFileInfo(FilenameUtils.getBaseName(imageFile.getPath()));
+ }
+
+ /**
+ * Extracts useful information from dataset image file name specific to iBrain2.
+ */
+ static ImageFileInfo extractBZImageFileInfo(String text)
+ {
+ String[] namedParts = StringUtils.split(text, "_");
+ final String plateLocationToken = StringUtils.split(namedParts[3], "-")[1];
+ final String wellLocationToken = StringUtils.split(namedParts[4], "-")[1];
+ final String timepointToken = StringUtils.split(namedParts[5], "-")[1];
+ final String channelToken = StringUtils.split(namedParts[6], "-")[1];
+ ImageFileInfo info = new ImageFileInfo();
+ info.setPlateLocationToken(plateLocationToken);
+ info.setWellLocationToken(wellLocationToken);
+ info.setChannelToken(channelToken);
+ info.setTimepointToken(timepointToken);
+ return info;
+ }
+
+ static IEntityProperty[] createVocabularyProperty(String propertyTypeCode, String termCode)
+ {
+ List<IEntityProperty> sampleProperties = new ArrayList<IEntityProperty>();
+ VocabularyTermValueEntityProperty property = new VocabularyTermValueEntityProperty();
+ VocabularyTerm vocabularyTerm = new VocabularyTerm();
+ vocabularyTerm.setCode(termCode);
+ property.setVocabularyTerm(vocabularyTerm);
+ PropertyType propertyType = new PropertyType();
+ DataType dataType = new DataType();
+ dataType.setCode(DataTypeCode.CONTROLLEDVOCABULARY);
+ propertyType.setDataType(dataType);
+ propertyType.setCode(propertyTypeCode);
+ property.setPropertyType(propertyType);
+ sampleProperties.add(property);
+ return sampleProperties.toArray(new IEntityProperty[sampleProperties.size()]);
+ }
+
+ static IEntityProperty[] createVarcharProperty(String propertyTypeCode, String description)
+ {
+ List<IEntityProperty> properties = new ArrayList<IEntityProperty>();
+ GenericValueEntityProperty property = new GenericValueEntityProperty();
+ property.setValue(description);
+ PropertyType propertyType = new PropertyType();
+ DataType dataType = new DataType();
+ dataType.setCode(DataTypeCode.VARCHAR);
+ propertyType.setDataType(dataType);
+ propertyType.setCode(propertyTypeCode);
+ property.setPropertyType(propertyType);
+ properties.add(property);
+ return properties.toArray(new IEntityProperty[properties.size()]);
+ }
+
+ static NewSample createPlate(SampleIdentifier sampleIdentifier,
+ ExperimentIdentifier experimentIdentifier, String plateGeometry)
+ {
+ NewSample sample = new NewSample();
+ sample.setExperimentIdentifier(experimentIdentifier.toString());
+ sample.setIdentifier(sampleIdentifier.toString());
+ SampleType sampleType = new SampleType();
+ sampleType.setCode(ScreeningConstants.PLATE_PLUGIN_TYPE_CODE);
+ sample.setSampleType(sampleType);
+ sample.setProperties(createVocabularyProperty(ScreeningConstants.PLATE_GEOMETRY,
+ plateGeometry));
+ return sample;
+ }
+
+ static List<Location> extractPlateLocations(File incomingDataSetPath)
+ {
+ List<File> imageFiles = ImageFileExtractorUtils.listImageFiles(incomingDataSetPath);
+ List<Location> plateLocations = new ArrayList<Location>();
+ for (File imageFile : imageFiles)
+ {
+ String baseName = FilenameUtils.getBaseName(imageFile.getPath());
+ String plateLocationToken = extractBZImageFileInfo(baseName).getPlateLocationToken();
+ plateLocations.add(Location
+ .tryCreateLocationFromTransposedMatrixCoordinate(plateLocationToken));
+ }
+ return plateLocations;
+ }
+
+ static NewExperiment createExperimentSIRNAHCS(ExperimentIdentifier experimentIdentifier)
+ {
+ NewExperiment experiment = new NewExperiment();
+ experiment.setExperimentTypeCode(ScreeningConstants.SIRNA_HCS);
+ experiment.setIdentifier(experimentIdentifier.toString());
+ experiment.setProperties(createVarcharProperty(ScreeningConstants.DESCRIPTION, "-"));
+ return experiment;
+
+ }
+
+}
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/biozentrum/PlateGeometryOracleTest.java
new file mode 100644
index 00000000000..59bf015a32d
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/PlateGeometryOracleTest.java
@@ -0,0 +1,152 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
+
+import java.util.Arrays;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * Test cases from {@link PlateGeometryOracle}.
+ *
+ * @author Izabela Adamczyk
+ */
+public class PlateGeometryOracleTest extends AssertJUnit
+{
+
+ private static final String GEOMETRY_3X4 = "12_3X4";
+
+ private static final String GEOMETRY_12_WELLS_3X4 = "12_WELLS_3X4";
+
+ private static final String GEOMETRY_12_WELLS_4X3 = "12_WELLS_4X3";
+
+ private static final String GEOMETRY_16_WELLS_4X4 = "16_WELLS_4X4";
+
+ private static final String GEOMETRY_1200_WELLS_40X30 = "1200_WELLS_40X30";
+
+ @Test
+ public void testTwoSimilarMatchingGeometriesGetFirst() throws Exception
+ {
+ assertEquals(GEOMETRY_12_WELLS_3X4, PlateGeometryOracle.figureGeometry(Arrays
+ .asList(new Location(1, 1)), Arrays.asList(GEOMETRY_12_WELLS_3X4,
+ GEOMETRY_12_WELLS_4X3)));
+ assertEquals(GEOMETRY_12_WELLS_4X3, PlateGeometryOracle.figureGeometry(Arrays
+ .asList(new Location(1, 1)), Arrays.asList(GEOMETRY_12_WELLS_4X3,
+ GEOMETRY_12_WELLS_3X4)));
+ }
+
+ @Test
+ public void testGetSmallerGeometry() throws Exception
+ {
+ assertEquals(GEOMETRY_12_WELLS_3X4, PlateGeometryOracle.figureGeometry(Arrays
+ .asList(new Location(1, 1)), Arrays.asList(GEOMETRY_1200_WELLS_40X30,
+ GEOMETRY_12_WELLS_3X4)));
+ }
+
+ @Test
+ public void testGetSmallestMatchingGeometry() throws Exception
+ {
+ assertEquals(GEOMETRY_1200_WELLS_40X30, PlateGeometryOracle.figureGeometry(Arrays
+ .asList(new Location(3, 4)), Arrays.asList(GEOMETRY_12_WELLS_3X4,
+ GEOMETRY_1200_WELLS_40X30)));
+ }
+
+ @Test
+ public void testGetSmallestMatchingGeometryForManyLocations() throws Exception
+ {
+ assertEquals(GEOMETRY_12_WELLS_4X3, PlateGeometryOracle.figureGeometry(Arrays.asList(
+ new Location(1, 1), new Location(3, 4)), Arrays.asList(GEOMETRY_12_WELLS_3X4,
+ GEOMETRY_12_WELLS_4X3, GEOMETRY_1200_WELLS_40X30)));
+ }
+
+ @Test
+ public void testGetSmallestMatchingGeometryForManyLocationsWithSimilarGeometries()
+ throws Exception
+ {
+ assertEquals(GEOMETRY_1200_WELLS_40X30, PlateGeometryOracle.figureGeometry(Arrays.asList(
+ new Location(1, 1), new Location(3, 4), new Location(4, 3)), Arrays.asList(
+ GEOMETRY_12_WELLS_3X4, GEOMETRY_12_WELLS_4X3, GEOMETRY_1200_WELLS_40X30)));
+ }
+
+ @Test
+ public void testGetSmallestMatchingGeometryForManyLocationsWithGeometryMatchingMaxLocations()
+ throws Exception
+ {
+ assertEquals(GEOMETRY_16_WELLS_4X4, PlateGeometryOracle.figureGeometry(Arrays.asList(
+ new Location(1, 1), new Location(3, 4), new Location(4, 3)), Arrays.asList(
+ GEOMETRY_12_WELLS_3X4, GEOMETRY_12_WELLS_4X3, GEOMETRY_1200_WELLS_40X30,
+ GEOMETRY_16_WELLS_4X4)));
+ }
+
+ @Test
+ public void testSimpleGeometryCode() throws Exception
+ {
+ assertEquals(GEOMETRY_3X4, PlateGeometryOracle.figureGeometry(Arrays.asList(new Location(1,
+ 2)), Arrays.asList(GEOMETRY_3X4)));
+
+ }
+
+ @Test
+ public void testOneLocationOneGeometryMatching() throws Exception
+ {
+ assertEquals(GEOMETRY_12_WELLS_3X4, PlateGeometryOracle.figureGeometry(Arrays
+ .asList(new Location(1, 2)), Arrays.asList(GEOMETRY_12_WELLS_3X4)));
+
+ }
+
+ @Test
+ public void testOneLocationOneGeometryMatchingMaxValues() throws Exception
+ {
+ assertEquals(GEOMETRY_12_WELLS_3X4, PlateGeometryOracle.figureGeometry(Arrays
+ .asList(new Location(4, 3)), Arrays.asList(GEOMETRY_12_WELLS_3X4)));
+ }
+
+ @Test
+ public void testOneLocationOneGeometryNotMatchingY() throws Exception
+ {
+ boolean exceptionThrown = false;
+ try
+ {
+ PlateGeometryOracle.figureGeometry(Arrays.asList(new Location(3, 4)), Arrays
+ .asList(GEOMETRY_12_WELLS_3X4));
+ } catch (UserFailureException ex)
+ {
+ exceptionThrown = true;
+ }
+ assertTrue(exceptionThrown);
+ }
+
+ @Test
+ public void testOneLocationOneGeometryNotMatchingX() throws Exception
+ {
+ boolean exceptionThrown = false;
+ try
+ {
+ PlateGeometryOracle.figureGeometry(Arrays.asList(new Location(5, 3)), Arrays
+ .asList(GEOMETRY_12_WELLS_3X4));
+ } catch (UserFailureException ex)
+ {
+ exceptionThrown = true;
+ }
+ assertTrue(exceptionThrown);
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/UtilsTest.java
similarity index 81%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractorTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/UtilsTest.java
index c2dc6e560ed..225cf3fd993 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/HCSImageFileExtractorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/UtilsTest.java
@@ -23,19 +23,18 @@ import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor.ImageFileInfo;
/**
- * Test cases for {@link HCSImageFileExtractor}.
+ * Test cases for {@link Utils}.
*
* @author Izabela Adamczyk
*/
-@Friend(toClasses = HCSImageFileExtractor.class)
-public class HCSImageFileExtractorTest extends AssertJUnit
+@Friend(toClasses = Utils.class)
+public class UtilsTest extends AssertJUnit
{
@Test
public void testExtractFileInfoCorrectFileName() throws Exception
{
ImageFileInfo info =
- HCSImageFileExtractor
- .extractFileInfo("SM100719invasomes_plt-1_bc-UNK_wp-A01_s-10_t-1_wl-Cy3_001");
+ Utils.extractBZImageFileInfo("SM100719invasomes_plt-1_bc-UNK_wp-A01_s-10_t-1_wl-Cy3_001");
assertEquals("plate location token", "A01", info.getPlateLocationToken());
assertEquals("channel token", "Cy3", info.getChannelToken());
assertEquals("time point token", "1", info.getTimepointToken());
--
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