From b4f620a673d7a41cfa708cdd5bc68452fcff3ef2 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 23 Apr 2010 13:59:51 +0000
Subject: [PATCH] [LMS-1491] listing feature vectors; introduced
CsvFileReaderHelper
SVN: 15605
---
.../server/TabularDataGraphServlet.java | 37 +--
...bularDataGraphCollectionConfiguration.java | 12 +-
.../server/DssServiceRpcScreening.java | 212 +++++++++++++++++-
.../shared/api/v1/dto/FeatureVector.java | 7 +
.../api/v1/dto/FeatureVectorDataset.java | 18 ++
.../cisd/utils/CsvFileReaderHelper.java | 152 +++++++++++++
.../server/DssServiceRpcScreeningTest.java | 130 +++++++++++
7 files changed, 526 insertions(+), 42 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/utils/CsvFileReaderHelper.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 0e9ce3ec0fc..5a57b75a30f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -17,12 +17,8 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.File;
-import java.io.FileInputStream;
import java.io.IOException;
-import java.nio.charset.Charset;
-import java.util.ArrayList;
import java.util.Enumeration;
-import java.util.List;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
@@ -30,12 +26,11 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;
-import com.csvreader.CsvReader;
-
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.server.graph.ITabularDataGraph;
import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphCollectionConfiguration;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.utils.CsvFileReaderHelper;
/**
* @author Chandrasekhar Ramakrishnan
@@ -185,34 +180,6 @@ public class TabularDataGraphServlet extends AbstractDatasetDownloadServlet
*/
private DatasetFileLines getDatasetFileLines(String path) throws IOException
{
- File file = new File(path);
- CsvReader reader = getCsvReader(file);
- List<String[]> lines = new ArrayList<String[]>();
- while (reader.readRecord())
- {
- lines.add(reader.getValues());
- }
-
- return new DatasetFileLines(file, path, lines);
- }
-
- /**
- * Get a CsvReader for parsing a tabular data file.
- */
- private CsvReader getCsvReader(File file) throws IOException
- {
- if (file.isFile() == false)
- {
- throw new UserFailureException(file + " does not exist or is not a file.");
- }
- FileInputStream fileInputStream = new FileInputStream(file);
-
- CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
- csvReader.setDelimiter(configuration.getColumnDelimiter());
- csvReader.setSkipEmptyRecords(true);
- csvReader.setUseComments(configuration.isIgnoreComments());
- csvReader.setComment(configuration.getCommentDelimiter());
-
- return csvReader;
+ return CsvFileReaderHelper.getDatasetFileLines(new File(path), configuration);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
index 77b57e02b1d..32297581ed5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
@@ -32,11 +32,12 @@ import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphConfigu
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PropertyParametersUtil;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PropertyParametersUtil.SectionProperties;
+import ch.systemsx.cisd.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class TabularDataGraphCollectionConfiguration
+public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderConfiguration
{
private static final String SEPARATOR_PROPERTY_KEY = "separator";
@@ -252,9 +253,6 @@ public class TabularDataGraphCollectionConfiguration
return columnDelimiter;
}
- /**
- * Should comments be ignored?
- */
public boolean isIgnoreComments()
{
return ignoreComments;
@@ -265,6 +263,11 @@ public class TabularDataGraphCollectionConfiguration
return comment;
}
+ public boolean isSkipEmptyRecords()
+ {
+ return true;
+ }
+
public int getImageWidth()
{
return imageWidth;
@@ -289,4 +292,5 @@ public class TabularDataGraphCollectionConfiguration
{
return graphNames;
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index e78779680fb..97046e3fc7f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -19,9 +19,18 @@ package ch.systemsx.cisd.openbis.dss.screening.server;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
+import java.io.IOException;
import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import com.csvreader.CsvReader;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.HCSDatasetLoader;
@@ -29,16 +38,20 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.utils.CsvFileReaderHelper;
/**
* Implementation of the screening API interface using RPC. The instance will be created in spring
@@ -72,11 +85,44 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public List<String> listAvailableFeatureNames(String sessionToken,
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
{
- // TODO Auto-generated method stub
-
+ try
+ {
+ List<String> result = new ArrayList<String>(); // keep the order
+ for (IFeatureVectorDatasetIdentifier dataset : featureDatasets)
+ {
+ // add only new feature names
+ String[] featureNames = extractFeatureNames(sessionToken, dataset);
+ for (String featureName : featureNames)
+ {
+ if (result.contains(featureName) == false)
+ {
+ result.add(featureName);
+ }
+ }
+ }
+ return result;
+ } catch (IOException ex)
+ {
+ // FIXME handle exceptions
+ ex.printStackTrace();
+ }
return null;
}
+ private String[] extractFeatureNames(String sessionToken,
+ IFeatureVectorDatasetIdentifier dataset) throws IOException
+ {
+ return extractFeatureNames(getDatasetFile(sessionToken, dataset));
+ }
+
+ private File getDatasetFile(String sessionToken, IDatasetIdentifier dataset)
+ {
+ // FIXME return file in subdirectory
+ return checkAccessAndGetRootDirectory(sessionToken, dataset.getDatasetCode());
+ }
+
+ //
+
public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
List<? extends IImageDatasetIdentifier> imageDatasets)
{
@@ -88,10 +134,30 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets,
List<String> featureNames)
{
- // TODO Auto-generated method stub
+ try
+ {
+ List<FeatureVectorDataset> result = new ArrayList<FeatureVectorDataset>();
+
+ for (IFeatureVectorDatasetIdentifier dataset : featureDatasets)
+ {
+ result.add(createFeatureVectorDataset(sessionToken, dataset, featureNames));
+ }
+ return result;
+ } catch (IOException ex)
+ {
+ // FIXME handle exceptions
+ ex.printStackTrace();
+ }
return null;
}
+ private FeatureVectorDataset createFeatureVectorDataset(String sessionToken,
+ IFeatureVectorDatasetIdentifier dataset, List<String> featureNames) throws IOException
+ {
+ return createFeatureVectorDataset(getDatasetFile(sessionToken, dataset), dataset,
+ featureNames);
+ }
+
public InputStream loadImage(String sessionToken, PlateImageReference imageReference)
{
ExternalData imageDataset =
@@ -193,4 +259,144 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return dataset.getDataSetType().getCode().equals(ScreeningConstants.IMAGE_DATASET_TYPE);
}
+ //
+ // helper methods and classes
+ //
+
+ // exposed for testing
+ static String[] extractFeatureNames(File datasetFile) throws IOException
+ {
+ CsvReader reader = null;
+ try
+ {
+ reader = CsvFileReaderHelper.getCsvReader(datasetFile);
+ if (reader.readHeaders())
+ {
+ return reader.getHeaders();
+ }
+ return new String[0]; // empty file
+ } finally
+ {
+ if (reader != null)
+ {
+ reader.close();
+ }
+ }
+ }
+
+ // exposed for testing
+ static FeatureVectorDataset createFeatureVectorDataset(File datasetFile,
+ IFeatureVectorDatasetIdentifier dataset, List<String> featureNames) throws IOException
+ {
+ DatasetFileLines fileLines = CsvFileReaderHelper.getDatasetFileLines(datasetFile);
+ String[] headerTokens = fileLines.getHeaderTokens();
+
+ List<String> existingFeatureNames = new ArrayList<String>();
+ Set<String> columnNames = new HashSet<String>(Arrays.asList(headerTokens));
+ for (String featureName : featureNames)
+ {
+ if (columnNames.contains(featureName))
+ {
+ existingFeatureNames.add(featureName);
+ }
+ }
+
+ Map<String, Integer> indexByName = new HashMap<String, Integer>();
+ for (int i = 0; i < headerTokens.length; i++)
+ {
+ indexByName.put(headerTokens[i].toLowerCase(), i);
+ }
+
+ FeatureVectorDatasetBuilder builder =
+ new FeatureVectorDatasetBuilder(dataset, existingFeatureNames);
+ for (String[] dataLine : fileLines.getDataLines())
+ {
+ FeatureVector vector =
+ tryExtractFeatureVector(dataLine, indexByName, existingFeatureNames);
+ if (vector != null)
+ {
+ builder.addFeatureVector(vector);
+ } else
+ {
+ operationLog.warn("wrong format or well not found");
+ }
+ }
+ return builder.create();
+ }
+
+ private static FeatureVector tryExtractFeatureVector(String[] dataLine,
+ Map<String, Integer> indexByName, List<String> featureNames)
+ {
+ WellPosition wellPositionOrNull = tryExtractWellPosition(dataLine, indexByName);
+
+ if (wellPositionOrNull != null)
+ {
+ double[] values = new double[featureNames.size()];
+ for (int i = 0; i < featureNames.size(); i++)
+ {
+ try
+ {
+ int index = indexByName.get(featureNames.get(i));
+ values[i] = Double.parseDouble(dataLine[index]);
+ } catch (NumberFormatException ex)
+ {
+ // skip this feature
+ return null;
+ }
+ }
+ return new FeatureVector(wellPositionOrNull, values);
+ }
+ return null;
+ }
+
+ private static WellPosition tryExtractWellPosition(String[] fileLine,
+ Map<String, Integer> indexByName)
+ {
+ String coordinate;
+ Integer wellIndexOrNull = indexByName.get("WellName".toLowerCase());
+ if (wellIndexOrNull != null)
+ {
+ coordinate = fileLine[wellIndexOrNull];
+ } else
+ {
+ Integer rowIndexOrNull = indexByName.get("row".toLowerCase());
+ Integer colIndexOrNull = indexByName.get("col".toLowerCase());
+ if (rowIndexOrNull == null || colIndexOrNull == null)
+ {
+ operationLog.warn("well position missing");
+ return null;
+ }
+ coordinate = fileLine[rowIndexOrNull] + fileLine[colIndexOrNull];
+ }
+
+ Location location = Location.tryCreateLocationFromMatrixCoordinate(coordinate);
+ return new WellPosition(location.getY(), location.getX());
+ }
+
+ private static class FeatureVectorDatasetBuilder
+ {
+ private final IFeatureVectorDatasetIdentifier dataset;
+
+ private final List<String> featureNames;
+
+ private final List<FeatureVector> featureVectors;
+
+ public FeatureVectorDatasetBuilder(IFeatureVectorDatasetIdentifier dataset,
+ List<String> featureNames)
+ {
+ this.dataset = dataset;
+ this.featureNames = featureNames;
+ this.featureVectors = new ArrayList<FeatureVector>();
+ }
+
+ public void addFeatureVector(FeatureVector vector)
+ {
+ featureVectors.add(vector);
+ }
+
+ public FeatureVectorDataset create()
+ {
+ return new FeatureVectorDataset(dataset, featureNames, featureVectors);
+ }
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVector.java
index 6d35e3a512b..a68a1a0b5a3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVector.java
@@ -1,6 +1,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
import java.io.Serializable;
+import java.util.Arrays;
/**
* Feature vector for one well.
@@ -32,4 +33,10 @@ public class FeatureVector implements Serializable
{
return values;
}
+
+ @Override
+ public String toString()
+ {
+ return "wellPosition: " + wellPosition + ", values: " + Arrays.toString(values);
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java
index 5dfde08b5ff..bb13e2ec41f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java
@@ -43,4 +43,22 @@ public class FeatureVectorDataset implements Serializable
{
return featureVectors;
}
+
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("datasetCode: " + dataset.getDatasetCode());
+ sb.append(", storeUrl: " + dataset.getDatastoreServerUrl());
+ sb.append("\n\tfeatures: ");
+ for (int i = 0; i < featureNames.size(); i++)
+ {
+ sb.append(featureNames.get(i) + ", ");
+ }
+ for (int i = 0; i < featureVectors.size(); i++)
+ {
+ sb.append("\n\t" + featureVectors.get(i));
+ }
+ return sb.toString();
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/utils/CsvFileReaderHelper.java b/screening/source/java/ch/systemsx/cisd/utils/CsvFileReaderHelper.java
new file mode 100644
index 00000000000..1bc83d35184
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/utils/CsvFileReaderHelper.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.utils;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.csvreader.CsvReader;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+
+/**
+ * @author Piotr Buczek
+ */
+public class CsvFileReaderHelper
+{
+
+ /**
+ * Configuration for reading csv file.
+ *
+ * @author Piotr Buczek
+ */
+ public interface ICsvFileReaderConfiguration
+ {
+
+ public boolean isIgnoreComments();
+
+ public boolean isSkipEmptyRecords();
+
+ public char getColumnDelimiter();
+
+ public char getCommentDelimiter();
+ }
+
+ /**
+ * Get a CsvReader for parsing a tabular data file with default configuration.
+ */
+ public static CsvReader getCsvReader(File file) throws IOException
+ {
+ return getCsvReader(file, new DefaultCsvFileReaderConfiguration());
+ }
+
+ /**
+ * Get a CsvReader for parsing a tabular data file with specified <var>configuration</var>.
+ */
+ public static CsvReader getCsvReader(File file, ICsvFileReaderConfiguration configuration)
+ throws IOException
+ {
+ if (file.isFile() == false)
+ {
+ throw new UserFailureException(file + " does not exist or is not a file.");
+ }
+ FileInputStream fileInputStream = new FileInputStream(file);
+
+ CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
+ csvReader.setDelimiter(configuration.getColumnDelimiter());
+ csvReader.setUseComments(configuration.isIgnoreComments());
+ csvReader.setComment(configuration.getCommentDelimiter());
+ csvReader.setSkipEmptyRecords(configuration.isSkipEmptyRecords());
+
+ return csvReader;
+ }
+
+ /**
+ * Return the tabular data as a DatasetFileLines with default configuration.
+ */
+ public static DatasetFileLines getDatasetFileLines(File file) throws IOException
+ {
+ return getDatasetFileLines(file, new DefaultCsvFileReaderConfiguration());
+ }
+
+ /**
+ * Return the tabular data as a DatasetFileLines with specified <var>configuration</var>.
+ */
+ public static DatasetFileLines getDatasetFileLines(File file,
+ ICsvFileReaderConfiguration configuration) throws IOException
+ {
+ CsvReader reader = null;
+ try
+ {
+ reader = CsvFileReaderHelper.getCsvReader(file, configuration);
+ List<String[]> lines = new ArrayList<String[]>();
+
+ while (reader.readRecord())
+ {
+ lines.add(reader.getValues());
+ }
+
+ return new DatasetFileLines(file, file.getPath(), lines);
+ } finally
+ {
+ if (reader != null)
+ {
+ reader.close();
+ }
+ }
+ }
+
+ /**
+ * Default configuration for reading csv file:
+ * <ul>
+ * <li>';' - column delimiter
+ * <li>'#' - comment delimiter
+ * <li>ignoring empty records
+ * </ul>
+ *
+ * @author Piotr Buczek
+ */
+ public static class DefaultCsvFileReaderConfiguration implements ICsvFileReaderConfiguration
+ {
+
+ public char getColumnDelimiter()
+ {
+ return ';';
+ }
+
+ public char getCommentDelimiter()
+ {
+ return '#';
+ }
+
+ public boolean isIgnoreComments()
+ {
+ return true;
+ }
+
+ public boolean isSkipEmptyRecords()
+ {
+ return true;
+ }
+
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
new file mode 100644
index 00000000000..7ba1e20c2a2
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -0,0 +1,130 @@
+/*
+ * Copyright 2009 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.screening.server;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
+
+/**
+ * Test cases for the {@link DssServiceRpcScreening}.
+ *
+ * @author Piotr Buczek
+ */
+public class DssServiceRpcScreeningTest extends AbstractFileSystemTestCase
+{
+
+ private static final String EXAMPLE1 =
+ "wellName;f0;f1;f2\n" + "A01;1.0;1.1;1.2\n" + "C7;2.0;2.1;2.2\n" + "D7;3.0;3.1;3.2\n"
+ + "D8;A3.0;3.1;3.2\n";
+
+ private static final String EXAMPLE2 =
+ "row;col;f0;f1;f2\n" + "A;01;1.0;1.1;1.2\n" + "C;7;2.0;2.1;2.2\n" + "D;7;3.0;3.1;3.2\n"
+ + "D;8;A3.0;3.1;3.2\n";
+
+ @Test
+ public void testExtractFeatureNames()
+ {
+ File datasetFile = new File(workingDirectory, "scrDataset");
+ FileUtilities.writeToFile(datasetFile, EXAMPLE1);
+ try
+ {
+ String[] names = DssServiceRpcScreening.extractFeatureNames(datasetFile);
+ assertEquals("[wellName, f0, f1, f2]", Arrays.toString(names));
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ @Test
+ public void testCreateFeatureVectorDataset()
+ {
+ File datasetFile = new File(workingDirectory, "scrDataset");
+ final String datasetCode = "CODE";
+ final String url = "URL";
+ final String[] fileData =
+ { EXAMPLE1, EXAMPLE2 };
+ try
+ {
+ for (String data : fileData)
+ {
+ FileUtilities.writeToFile(datasetFile, data);
+ IFeatureVectorDatasetIdentifier dataset =
+ createFeatureVectorDatasetIdentifier(datasetCode, url);
+ FeatureVectorDataset result =
+ DssServiceRpcScreening.createFeatureVectorDataset(datasetFile, dataset,
+ Arrays.asList(new String[]
+ { "f0", "f2", "f3" }));
+
+ assertEquals(dataset, result.getDataset());
+
+ assertEquals(2, result.getFeatureNames().size());
+ assertEquals("f0", result.getFeatureNames().get(0));
+ assertEquals("f2", result.getFeatureNames().get(1));
+
+ assertEquals(3, result.getFeatureVectors().size());
+
+ assertEquals("[1, 1]", result.getFeatureVectors().get(0).getWellPosition()
+ .toString());
+ assertEquals("[1.0, 1.2]", Arrays.toString(result.getFeatureVectors().get(0)
+ .getValues()));
+
+ assertEquals("[3, 7]", result.getFeatureVectors().get(1).getWellPosition()
+ .toString());
+ assertEquals("[2.0, 2.2]", Arrays.toString(result.getFeatureVectors().get(1)
+ .getValues()));
+
+ assertEquals("[4, 7]", result.getFeatureVectors().get(2).getWellPosition()
+ .toString());
+ assertEquals("[3.0, 3.2]", Arrays.toString(result.getFeatureVectors().get(2)
+ .getValues()));
+ }
+
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private IFeatureVectorDatasetIdentifier createFeatureVectorDatasetIdentifier(
+ final String datasetCode, final String url)
+ {
+ return new IFeatureVectorDatasetIdentifier()
+ {
+
+ public String getDatasetCode()
+ {
+ return datasetCode;
+ }
+
+ public String getDatastoreServerUrl()
+ {
+ return url;
+ }
+
+ };
+ }
+
+}
--
GitLab